I: pbuilder: network access will be disabled during build I: Current time: Tue May 7 02:15:09 +14 2024 I: pbuilder-time-stamp: 1714997709 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sra-sdk_3.0.3+dfsg-7.dsc] I: copying [./sra-sdk_3.0.3+dfsg.orig.tar.xz] I: copying [./sra-sdk_3.0.3+dfsg-7.debian.tar.xz] I: Extracting source gpgv: Signature made Mon May 6 02:51:20 2024 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sra-sdk_3.0.3+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting sra-sdk in sra-sdk-3.0.3+dfsg dpkg-source: info: unpacking sra-sdk_3.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking sra-sdk_3.0.3+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying set_explicit_path_to_schemata.patch dpkg-source: info: applying python3 dpkg-source: info: applying skip_test_using_lots_of_memory.patch dpkg-source: info: applying find_ncbi-vdb-interfaces.patch dpkg-source: info: applying link_vdb_dynamically.patch dpkg-source: info: applying use_debian_packaged_re2.patch dpkg-source: info: applying use_debian_packaged_compression_libs.patch dpkg-source: info: applying fix_javadoc_build.patch dpkg-source: info: applying use_soversions.patch dpkg-source: info: applying label_online_tests.patch dpkg-source: info: applying prefer_dynamic_libraries.patch dpkg-source: info: applying fix_ngs-c++-underlinkage.patch dpkg-source: info: applying use_c_locale_for_comma.patch dpkg-source: info: applying no_sse4.2.patch dpkg-source: info: applying support_libre2-11.patch dpkg-source: info: applying auto-gitignore I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 6 12:15 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=1876efdf455b4f04b47678fee3413300 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1056693 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.w5pI1lC5/pbuilderrc_NOs0 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.w5pI1lC5/b2 --logfile b2/build.log sra-sdk_3.0.3+dfsg-7.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, d-shlibs, dh-python, javahelper, libabsl-dev, libncbi-vdb-dev (>= 3.0.1+dfsg~), libfuse-dev, libhdf5-dev, libmagic-dev, libre2-dev, libxml2-dev, libzstd-dev, liblzma-dev, libsam-extract-dev, markdown | libtext-markdown-perl | discount, maven-repo-helper, python3-all, python3-distutils, default-jdk, flex, bison dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on libabsl-dev; however: Package libabsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libncbi-vdb-dev (>= 3.0.1+dfsg~); however: Package libncbi-vdb-dev is not installed. pbuilder-satisfydepends-dummy depends on libfuse-dev; however: Package libfuse-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libmagic-dev; however: Package libmagic-dev is not installed. pbuilder-satisfydepends-dummy depends on libre2-dev; however: Package libre2-dev is not installed. pbuilder-satisfydepends-dummy depends on libxml2-dev; however: Package libxml2-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libsam-extract-dev; however: Package libsam-extract-dev is not installed. pbuilder-satisfydepends-dummy depends on markdown | libtext-markdown-perl | discount; however: Package markdown is not installed. Package libtext-markdown-perl is not installed. Package discount is not installed. pbuilder-satisfydepends-dummy depends on maven-repo-helper; however: Package maven-repo-helper is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-distutils; however: Package python3-distutils is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bison{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cmake{a} cmake-data{a} d-shlibs{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hdf5-helpers{a} hicolor-icon-theme{a} icu-devtools{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} libabsl-dev{a} libabsl20230802{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libasound2-data{a} libasound2t64{a} libassuan0{a} libatk1.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcairo2{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcom-err2{a} libcups2t64{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1t64{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libfuse-dev{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgtk2.0-0t64{a} libgtk2.0-common{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu-dev{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} liblzma-dev{a} libmagic-dev{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto7t64{a} libmbedtls14t64{a} libmbedx509-1t64{a} libmodule-runtime-perl{a} libmoo-perl{a} libncbi-vdb-dev{a} libncbi-vdb3{a} libncbi-wvdb-dev{a} libncbi-wvdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libnpth0t64{a} libnspr4{a} libnss3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libre2-10{a} libre2-dev{a} libreadline8t64{a} librhash0{a} librole-tiny-perl{a} librtmp1{a} libsam-extract-dev{a} libsam-extract3{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsensors-config{a} libsensors5{a} libsepol-dev{a} libsharpyuv0{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsub-quote-perl{a} libsz2{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libuv1t64{a} libvulkan1{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml2{a} libxml2-dev{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} markdown{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tzdata{a} wdiff{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf bzip2-doc curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra krb5-locales libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libfl-dev libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgmock-dev libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace unzip wget xdg-user-dirs 0 packages upgraded, 295 newly installed, 0 to remove and 0 not upgraded. Need to get 273 MB of archives. After unpacking 909 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 binfmt-support amd64 2.2.2-7 [64.3 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b2 [426 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 17 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.0-9 [1481 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b3 [138 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.41-4 [46.6 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 46.0-1 [614 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.52.0-1 [166 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 bison amd64 2:3.8.2+dfsg-1+b1 [1175 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 63 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 78 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 87 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 java-common all 0.75 [6640 B] Get: 94 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.2.0-1 [54.7 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 99 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 100 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-common all 2.24.33-4 [2661 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.52.0-1 [50.8 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [218 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [48.1 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [35.0 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.5-1+b1 [14.9 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.1-1+b1 [36.2 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b1 [15.5 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b1 [16.0 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1 [36.1 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libgtk2.0-0t64 amd64 2.24.33-4 [1816 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 144 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.6-1+b1 [36.6 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-1 [106 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-1 [106 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-1 [122 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-1 [105 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-1 [116 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-1 [108 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-1 [109 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 155 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.6-1+b1 [8279 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.6-1+b1 [151 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.11-1 [20.9 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.11-1+b1 [369 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1 [43.9 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b1 [25.9 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jre amd64 17.0.11+9-1 [185 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.17-75 [1056 B] Get: 178 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 179 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 180 http://deb.debian.org/debian unstable/main amd64 openjdk-17-jdk amd64 17.0.11+9-1 [10.4 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.17-75 [1068 B] Get: 182 http://deb.debian.org/debian unstable/main amd64 libassuan0 amd64 2.5.6-1+b1 [50.4 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.40-3 [565 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.6-1 [131 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.6-3.1 [17.9 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.40-3 [793 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 gnupg-utils amd64 2.2.40-3 [928 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.40-3 [950 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.2.1-3+b2 [78.3 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.40-3 [695 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 gpg-wks-client amd64 2.2.40-3 [541 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 gpg-wks-server amd64 2.2.40-3 [532 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.40-3 [671 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.40-3 [847 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 197 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libfile-touch-perl all 0.12-2 [8816 B] Get: 200 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libipc-run-perl all 20231003.0-2 [101 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1 [15.9 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.28-1 [98.6 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get: 228 http://deb.debian.org/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 wdiff amd64 1.2.2-6 [119 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 devscripts all 2.23.7 [1068 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 fastjar amd64 2:0.98-7 [80.1 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.10.10+repack-3.3 [23.4 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 jarwrapper all 0.79 [10.1 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 javahelper all 0.79 [84.6 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libabsl-dev amd64 20230802.1-4 [1208 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 252 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.7.1-5 [547 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.5-2+b1 [351 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.42-4+b1 [55.8 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.42-4+b1 [755 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.5-2+b2 [158 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libfuse-dev amd64 2.9.9-8.1 [1021 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.3 [89.3 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.3 [40.4 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.3 [21.3 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 275 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libmagic-dev amd64 1:5.45-3 [118 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libncbi-wvdb3 amd64 3.0.2+dfsg-2+b1 [1078 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libncbi-wvdb-dev amd64 3.0.2+dfsg-2+b1 [1186 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb-dev amd64 3.0.2+dfsg-2+b1 [1460 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libre2-10 amd64 20230301-3+b1 [188 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libre2-dev amd64 20230301-3+b1 [245 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libsam-extract3 amd64 3.0.2+dfsg-2+b1 [43.4 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libsam-extract-dev amd64 3.0.2+dfsg-2+b1 [44.8 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.3+b3 [787 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 markdown all 1.0.1-12 [17.7 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.11.8-1 [1056 B] Fetched 273 MB in 13s (21.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../0-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../1-binfmt-support_2.2.2-7_amd64.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package m4. Preparing to unpack .../2-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20221 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21213 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_amd64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../003-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../004-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../005-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../006-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. 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Preparing to unpack .../013-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../014-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package libgdk-pixbuf2.0-common. Preparing to unpack .../016-libgdk-pixbuf2.0-common_2.42.10+dfsg-3_all.deb ... Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../017-libglib2.0-0t64_2.80.0-9_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.80.0-9) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../018-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../019-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../020-shared-mime-info_2.4-4_amd64.deb ... Unpacking shared-mime-info (2.4-4) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../021-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../022-libpng16-16t64_1.6.43-5_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-5) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../023-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../024-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../025-liblerc4_4.0.0+ds-4+b1_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../026-libsharpyuv0_1.4.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../027-libwebp7_1.4.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../028-libtiff6_4.5.1+git230720-4_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-4) ... Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64. Preparing to unpack .../029-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3+b3_amd64.deb ... Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Selecting previously unselected package gtk-update-icon-cache. 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Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libzstd-dev:amd64 (1.5.5+dfsg2-2) ... Setting up bsdextrautils (2.40-8) ... Setting up libre2-10:amd64 (20230301-3+b1) ... Setting up hdf5-helpers (1.10.10+repack-3.3) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up java-common (0.75) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libclone-perl:amd64 (0.46-1+b2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:amd64 (1.7.0-1+b1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up libuv1t64:amd64 (1.48.0-1.1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.31-2) ... Setting up libsensors-config (1:3.6.0-9) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libassuan0:amd64 (2.5.6-1+b1) ... Setting up libmagic-dev:amd64 (1:5.45-3) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libpcre2-16-0:amd64 (10.42-4+b1) ... 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Setting up bison (2:3.8.2+dfsg-1+b1) ... update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b3) ... Setting up libgtk2.0-common (2.24.33-4) ... Setting up libsam-extract3:amd64 (3.0.2+dfsg-2+b1) ... Setting up cmake-data (3.29.2-2) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libre2-dev:amd64 (20230301-3+b1) ... Setting up openssl (3.2.1-3) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:amd64 (72.1-4+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liburi-perl (5.28-1) ... Setting up libsam-extract-dev:amd64 (3.0.2+dfsg-2+b1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up markdown (1.0.1-12) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up libnet-ssleay-perl:amd64 (1.94-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up flex (2.6.4-8.2+b2) ... Setting up libxcb1:amd64 (1.17.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-1) ... Setting up libatk1.0-0t64:amd64 (2.52.0-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libpcre2-dev:amd64 (10.42-4+b1) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.17.0-1) ... Setting up libselinux1-dev:amd64 (3.5-2+b2) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:amd64 (1.17.0-1) ... Setting up libedit2:amd64 (3.1-20230828-1+b1) ... Setting up libaec-dev:amd64 (1.1.3-1) ... Setting up libavahi-common3:amd64 (0.8-13+b2) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libxcb-shm0:amd64 (1.17.0-1) ... Setting up libfuse-dev:amd64 (2.9.9-8.1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:amd64 (1.17.0-1) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libllvm17t64:amd64 (1:17.0.6-12) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libxcb-sync1:amd64 (1.17.0-1) ... Setting up shared-mime-info (2.4-4) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libabsl-dev:amd64 (20230802.1-4) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libxcb-dri2-0:amd64 (1.17.0-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-4) ... Setting up libxcb-randr0:amd64 (1.17.0-1) ... Setting up libhtml-parser-perl:amd64 (3.82-1) ... Setting up gpgconf (2.2.40-3) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b3) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libxcomposite1:amd64 (1:0.4.5-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-1) ... Setting up gtk-update-icon-cache (3.24.41-4) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b1) ... Setting up gpg-agent (2.2.40-3) ... Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b3) ... Setting up gpgsm (2.2.40-3) ... Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.6-1+b1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-3) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libcurl4-openssl-dev:amd64 (8.7.1-5) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b1) ... Setting up libncbi-wvdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libxrandr2:amd64 (2:1.5.4-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gpg-wks-server (2.2.40-3) ... Setting up cmake (3.29.2-2) ... Setting up libncbi-wvdb-dev:amd64 (3.0.2+dfsg-2+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libglx-mesa0:amd64 (24.0.6-1+b1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libxcursor1:amd64 (1:1.2.1-1+b1) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.3) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up libgtk2.0-0t64:amd64 (2.24.33-4) ... Setting up gnupg (2.2.40-3) ... Setting up libncbi-vdb-dev:amd64 (3.0.2+dfsg-2+b1) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-setuptools (68.1.2-2) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-all (3.11.8-1) ... Setting up libhdf5-dev (1.10.10+repack-3.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up dh-python (6.20240422) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up javahelper (0.79) ... Processing triggers for libc-bin (2.38-7) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up maven-repo-helper (1.11) ... Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:amd64 (17.0.11+9-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.17-75) ... Setting up default-jdk (2:1.17-75) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sra-sdk_3.0.3+dfsg-7_source.changes dpkg-buildpackage: info: source package sra-sdk dpkg-buildpackage: info: source version 3.0.3+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Aaron M. Ucko dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=cmake \ --with python3,javahelper,jh_maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_auto_clean rm -rf ngs/ngs-java/x86_64-linux-gnu rm -rf ngs/ngs-bam/x86_64-linux-gnu rm -f ngs/ngs-bam/Makefile.config rm -f ngs/ngs-bam/Makefile.config.install.linux.x86_64.prl rm -f ngs/ngs-bam/Makefile.config.linux.x86_64 rm -f ngs/ngs-bam/reconfigure rm -rf ngs/ngs-sdk/ngs/unix/generic rm -rf ngs/ngs-sdk/x86_64-linux-gnu rm -rf ngs/ngs-python/build ngs/ngs-python/dist rm -rf ngs/ngs-python/ngs.egg-info find test tools -name actual -type d | xargs -rt rm -rf rm -rf ngs/ngs-*/examples/actual/* rm -fv test/*/*/tmp.kfg rm -rf libs/ngs-vdb/test/data/SparseFragmentBlobs rm -rf test/external/vdb-dump/data test/loaders/bam-load/out.sra find tools/loaders/general-loader/test -name input | xargs -rt rm -rf rm -f ngs/ngs-sdk/examples/actual.txt rm debian/libngs-jni.links rm: cannot remove 'debian/libngs-jni.links': No such file or directory make[1]: [debian/rules:45: override_dh_auto_clean] Error 1 (ignored) make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_autoreconf_clean -O--buildsystem=cmake jh_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake \ --with python3,javahelper,jh_maven_repo_helper dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_auto_configure -- -DVDB_LIBDIR=/usr/lib/x86_64-linux-gnu \ -DVDB_INCDIR=/usr/include/ncbi-vdb -DBUILD_TOOLS_LOADERS=ON \ -DBUILD_TOOLS_INTERNAL=ON -DBUILD_TOOLS_TEST_TOOLS=ON \ -DCMAKE_SKIP_RPATH=ON -DTOOLS_ONLY=OFF cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DVDB_LIBDIR=/usr/lib/x86_64-linux-gnu -DVDB_INCDIR=/usr/include/ncbi-vdb -DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON -DBUILD_TOOLS_TEST_TOOLS=ON -DCMAKE_SKIP_RPATH=ON -DTOOLS_ONLY=OFF .. CMAKE_VERSION=3.29.2 -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at build/env.cmake:32 (cmake_policy): The OLD behavior for policy CMP0115 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. Call Stack (most recent call first): CMakeLists.txt:62 (include) VERSION=3.0.3 -- Performing Test COMPILER_OPTION_SSE42_SUPPORTED -- Performing Test COMPILER_OPTION_SSE42_SUPPORTED - Success -- Found FLEX: /usr/bin/flex (found suitable version "2.6.4", minimum required is "2.6") -- Found BISON: /usr/bin/bison (found suitable version "3.8.2", minimum required is "3") -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") LIBXML2_INCLUDE_DIR=/usr/include/libxml2 LIBXML2_LIBRARIES=/usr/lib/x86_64-linux-gnu/libxml2.so -- Found Java: /usr/bin/java (found version "17.0.11") found components: Development -- Found Python3: /usr/bin/python3 (found version "3.11.9") found components: Interpreter Using ncbi-vdb interfaces: /usr/include/ncbi-vdb Using ncbi-vdb binary libraries: /usr/lib/x86_64-linux-gnu -- Looking for C++ include mbedtls/md.h -- Looking for C++ include mbedtls/md.h - not found RUN_SANITIZER_TESTS: OFF -- Found JNI: /usr/lib/jvm/default-java/include found components: AWT JVM BUILD_TOOLS_INTERNAL=ON BUILD_TOOLS_LOADERS=ON BUILD_TOOLS_TEST_TOOLS=ON CMake Warning at tools/external/sra-search/test/CMakeLists.txt:219 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-search is not found. The corresponding tests are skipped. -- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "3.2.2") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.10.10") found components: C CMake Warning at test/external/align-info/CMakeLists.txt:34 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/align-info is not found. The corresponding tests are skipped. CMake Warning at test/external/fasterq-dump/CMakeLists.txt:58 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/fasterq-dump is not found. The corresponding tests are skipped. CMake Warning at test/external/kdbmeta/CMakeLists.txt:43 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta is not found. The corresponding tests are skipped. CMake Warning at test/external/ngs-pileup/CMakeLists.txt:147 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ngs-pileup is not found. The corresponding tests are skipped. CMake Warning at test/external/prefetch/CMakeLists.txt:114 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/prefetch is not found. The corresponding tests are skipped. CMake Warning at test/external/sam-dump/CMakeLists.txt:51 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sam-dump is not found. The corresponding tests are skipped. CMake Warning at test/external/srapath/CMakeLists.txt:61 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/srapath is not found. The corresponding tests are skipped. CMake Warning at test/external/sra-pileup/CMakeLists.txt:50 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-pileup is not found. The corresponding tests are skipped. CMake Warning at test/external/sra-stat/CMakeLists.txt:61 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-stat is not found. The corresponding tests are skipped. CMake Warning at test/external/vdb-config/CMakeLists.txt:40 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config is not found. The corresponding tests are skipped. CMake Warning at test/external/vdb-validate/CMakeLists.txt:41 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-validate is not found. The corresponding tests are skipped. CMake Warning at test/loaders/bam-load/CMakeLists.txt:62 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/bam-load is not found. The corresponding tests are skipped. CMake Warning at test/loaders/fastq-loader/CMakeLists.txt:219 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/latf-load is not found. The corresponding tests are skipped. CMake Warning at test/loaders/kar/CMakeLists.txt:50 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kar is not found. The corresponding tests are skipped. CMake Warning at test/loaders/sra-sort/CMakeLists.txt:47 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sra-sort is not found. The corresponding tests are skipped. CMake Warning at test/internal/align-cache/CMakeLists.txt:42 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/align-cache is not found. The corresponding tests are skipped. CMake Warning at test/internal/copycat/CMakeLists.txt:68 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/copycat is not found. The corresponding tests are skipped. CMake Warning at test/internal/make-read-filter/CMakeLists.txt:72 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/make-read-filter is not found. The corresponding tests are skipped. CMake Warning at test/internal/read-filter-redact/CMakeLists.txt:40 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-unlock is not found. The corresponding tests are skipped. CMake Warning at test/internal/read-filter-redact/CMakeLists.txt:60 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/read-filter-redact is not found. The corresponding tests are skipped. CMake Warning at test/internal/vdb-copy/CMakeLists.txt:43 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-copy is not found. The corresponding tests are skipped. CMake Warning at test/internal/vdb-diff/CMakeLists.txt:75 (message): /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-diff is not found. The corresponding tests are skipped. -- Configuring done (12.4s) CMake Warning (dev) at tools/loaders/sharq/CMakeLists.txt:96 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (1.9s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' jh_linkjars -O--buildsystem=cmake dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sra-sdk-3.0.3+dfsg -B/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start 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ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/DependInfo.cmake "--color=" make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/DependInfo.cmake "--color=" make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++ /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ 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make -f shared/CMakeFiles/tk-version.dir/build.make shared/CMakeFiles/tk-version.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs/CMakeFiles/ngs.dir/build.make ngs/ncbi/ngs/CMakeFiles/ngs.dir/build make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build.make ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build.make ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/build [ 0%] Building C object shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"shared\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT shared/CMakeFiles/tk-version.dir/toolkit.vers.c.o -MF CMakeFiles/tk-version.dir/toolkit.vers.c.o.d -o CMakeFiles/tk-version.dir/toolkit.vers.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/shared/toolkit.vers.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build.make ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build.make ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/build [ 0%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o make -f ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build.make ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 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ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o [ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o -MF CMakeFiles/ngs.dir/NCBI-NGS.c.o.d -o CMakeFiles/ngs.dir/NCBI-NGS.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NCBI-NGS.c [ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o -MF CMakeFiles/ngs-jni.dir/jni_String.c.o.d -o CMakeFiles/ngs-jni.dir/jni_String.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_String.c [ 1%] Building C object ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o -MF CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_PileupEvent.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-py\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o -MF CMakeFiles/ngs-py.dir/py_Manager.c.o.d -o CMakeFiles/ngs-py.dir/py_Manager.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py/py_Manager.c make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/depend [ 1%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/DependInfo.cmake "--color=" [ 1%] Building C object ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-jni\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o -MF CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o.d -o CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni/jni_ErrorMsg.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o -MF CMakeFiles/ngs.dir/CSRA1_Pileup.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Pileup.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o cd 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/DependInfo.cmake "--color=" [ 1%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o [ 1%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o -MF CMakeFiles/ngs.dir/CSRA1_Alignment.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Alignment.c [ 1%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o [ 2%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG 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-I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReferenceWindow.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadCollection.cpp [ 2%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build.make ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/build [ 2%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp [ 3%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceSequenceItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadCollectionItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReferenceItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build.make ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/build [ 4%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Linking C static library ../ilib/libtk-version.a [ 4%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadCollectionItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -P CMakeFiles/tk-version.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/shared && /usr/bin/cmake -E cmake_link_script CMakeFiles/tk-version.dir/link.txt --verbose=1 In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadCollectionItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadCollection.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /usr/bin/ar qc ../ilib/libtk-version.a "CMakeFiles/tk-version.dir/toolkit.vers.c.o" [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o /usr/bin/ranlib ../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o -MF CMakeFiles/ngs.dir/CSRA1_Reference.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Reference.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Reference.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceSequence.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceSequence.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_AlignmentIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReferenceIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReferenceIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 4%] Built target tk-version [ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/DependInfo.cmake "--color=" [ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp [ 4%] Linking C static library ../../../ilib/libngs-py.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -P CMakeFiles/ngs-py.dir/cmake_clean_target.cmake [ 4%] Linking C static library ../../../ilib/libngs-jni.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-java.dir/build.make ngs/ngs-java/CMakeFiles/ngs-java.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -P CMakeFiles/ngs-jni.dir/cmake_clean_target.cmake make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-py && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-py.dir/link.txt --verbose=1 [ 4%] Building Java objects for ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClearClassFiles.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-jni && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-jni.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../ilib/libngs-py.a "CMakeFiles/ngs-py.dir/py_Manager.c.o" In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Reference.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javac -classpath :/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -d /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -h ./jni @/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_sources /usr/bin/ranlib ../../../ilib/libngs-py.a /usr/bin/ar qc ../../../ilib/libngs-jni.a "CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "CMakeFiles/ngs-jni.dir/jni_String.c.o" "CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" /usr/bin/ranlib ../../../ilib/libngs-jni.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target ngs-py make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Built target ngs-jni make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/kxml /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml/CMakeFiles/kxml.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc_javadoc.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/javadoc -d /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc -sourcepath "/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java" gov.nih.nlm.ncbi.ngs ngs In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/kxml/CMakeFiles/kxml.dir/build.make libs/kxml/CMakeFiles/kxml.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 4%] Building C object libs/kxml/CMakeFiles/kxml.dir/xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/kxml/CMakeFiles/kxml.dir/xml.c.o -MF CMakeFiles/kxml.dir/xml.c.o.d -o CMakeFiles/kxml.dir/xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/kxml/xml.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceSequenceItf; C = NGS_ReferenceSequence_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ [ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -MF CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_ReadCollection.c [ 4%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o -MF CMakeFiles/ngs.dir/CSRA1_Read.c.o.d -o CMakeFiles/ngs.dir/CSRA1_Read.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/CSRA1_Read.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadCollectionItf; C = NGS_ReadCollection_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Pileup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Pileup.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReferenceItf; C = NGS_Reference_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 4%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp [ 4%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupItf.cpp [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/EBI_ReferenceSequence.c [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEventIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEventIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/PileupEvent.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/PileupEvent.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o -MF CMakeFiles/ngs.dir/SRA_Statistics.c.o.d -o CMakeFiles/ngs.dir/SRA_Statistics.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_Statistics.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/AlignmentIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_DB_ReadCollection.c [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o -MF CMakeFiles/ngs.dir/SRA_Read.c.o.d -o CMakeFiles/ngs.dir/SRA_Read.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_Read.c [ 5%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroup.c [ 5%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp [ 5%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PileupEventItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_FragmentIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceIteratorItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 6%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Alignment.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -MF CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadGroupInfo.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PackageItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 7%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/PileupEventItf.cpp [ 7%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -MF CMakeFiles/ngs.dir/SRA_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReadCollection.c [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/SRA_ReferenceSequence.c [ 7%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc-parsexml.c.o -MF CMakeFiles/kxml.dir/xtoc-parsexml.c.o.d -o CMakeFiles/kxml.dir/xtoc-parsexml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc-parsexml.c [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o -MF CMakeFiles/ngs.dir/NGS_Statistics.c.o.d -o CMakeFiles/ngs.dir/NGS_Statistics.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Statistics.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupItf; C = NGS_Pileup_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupItf; C = NGS_Pileup_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroupIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Loading source files for package gov.nih.nlm.ncbi.ngs... Loading source files for package ngs... [ 7%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o [ 7%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -MF CMakeFiles/ngs.dir/NGS_ReadCollection.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadCollection.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp [ 7%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp [ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/ReadGroup.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -MF CMakeFiles/ngs.dir/NGS_PileupEvent.c.o.d -o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_PileupEvent.c [ 8%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp [ 8%] Building C object libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/kxml\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/kxml/CMakeFiles/kxml.dir/xtoc.c.o -MF CMakeFiles/kxml.dir/xtoc.c.o.d -o CMakeFiles/kxml.dir/xtoc.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/kxml/xtoc.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/AlignmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/AlignmentItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::PileupEventItf; C = NGS_PileupEvent_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o [ 8%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o -MF CMakeFiles/ngs.dir/NGS_Pileup.c.o.d -o CMakeFiles/ngs.dir/NGS_Pileup.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Pileup.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp [ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Read.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Read.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp [ 8%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp [ 8%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -MF CMakeFiles/ngs.dir/NGS_ReadGroup.c.o.d -o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReadGroup.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupEventIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Constructing Javadoc information... [ 9%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o -MF CMakeFiles/ngs.dir/NGS_Alignment.c.o.d -o CMakeFiles/ngs.dir/NGS_Alignment.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Alignment.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Read.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 9%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/FragmentIterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader/CMakeFiles/loader.dir/DependInfo.cmake "--color=" [ 10%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o -MF CMakeFiles/ngs.dir/NGS_Reference.c.o.d -o CMakeFiles/ngs.dir/NGS_Reference.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Reference.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/loader/CMakeFiles/loader.dir/build.make libs/loader/CMakeFiles/loader.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadGroupItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 10%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp [ 10%] Building C object libs/loader/CMakeFiles/loader.dir/progressbar.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/progressbar.c.o -MF CMakeFiles/loader.dir/progressbar.c.o.d -o CMakeFiles/loader.dir/progressbar.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/progressbar.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Fragment.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 10%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceItf.cpp [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceSequence.c [ 10%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp [ 10%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o -MF CMakeFiles/ngs.dir/NGS_Fragment.c.o.d -o CMakeFiles/ngs.dir/NGS_Fragment.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Fragment.c [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o -MF CMakeFiles/ngs.dir/NGS_Read.c.o.d -o CMakeFiles/ngs.dir/NGS_Read.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Read.c [ 10%] Building C object libs/loader/CMakeFiles/loader.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/loader-file.c.o -MF CMakeFiles/loader.dir/loader-file.c.o.d -o CMakeFiles/loader.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/loader-file.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Statistics.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/Statistics.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::AlignmentItf; C = NGS_Alignment_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 10%] Building C object libs/loader/CMakeFiles/loader.dir/loader-meta.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/loader-meta.c.o -MF CMakeFiles/loader.dir/loader-meta.c.o.d -o CMakeFiles/loader.dir/loader-meta.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/loader-meta.c [ 10%] Building C object libs/loader/CMakeFiles/loader.dir/queue-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/queue-file.c.o -MF CMakeFiles/loader.dir/queue-file.c.o.d -o CMakeFiles/loader.dir/queue-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/queue-file.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadGroupItf; C = NGS_ReadGroup_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 10%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o [ 10%] Linking C static library ../../ilib/libkxml.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o -MF CMakeFiles/ngs.dir/NGS_Cursor.c.o.d -o CMakeFiles/ngs.dir/NGS_Cursor.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Cursor.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -P CMakeFiles/kxml.dir/cmake_clean_target.cmake [ 10%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/kxml && /usr/bin/cmake -E cmake_link_script CMakeFiles/kxml.dir/link.txt --verbose=1 [ 10%] Building C object libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/alignment-writer.c.o -MF CMakeFiles/loader.dir/alignment-writer.c.o.d -o CMakeFiles/loader.dir/alignment-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/alignment-writer.c /usr/bin/ar qc ../../ilib/libkxml.a CMakeFiles/kxml.dir/xml.c.o "CMakeFiles/kxml.dir/xtoc-parsexml.c.o" CMakeFiles/kxml.dir/xtoc.c.o /usr/bin/ranlib ../../ilib/libkxml.a [ 10%] Building CXX object ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -MF CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o.d -o CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 10%] Built target kxml make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_PileupIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 11%] Building C object libs/loader/CMakeFiles/loader.dir/common-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/common-reader.c.o -MF CMakeFiles/loader.dir/common-reader.c.o.d -o CMakeFiles/loader.dir/common-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/common-reader.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build.make libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 11%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o [ 11%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c [ 11%] Building C object libs/loader/CMakeFiles/loader.dir/common-writer.c.o In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/c++/StringRef.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/common-writer.c.o -MF CMakeFiles/loader.dir/common-writer.c.o.d -o CMakeFiles/loader.dir/common-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/common-writer.c make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build.make libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/build In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReferenceSequenceItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 11%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp [ 11%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o Creating destination directory: "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp [ 11%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlobIterator.cpp [ 11%] Building C object libs/loader/CMakeFiles/loader.dir/mmarray.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/mmarray.c.o -MF CMakeFiles/loader.dir/mmarray.c.o.d -o CMakeFiles/loader.dir/mmarray.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/mmarray.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReadCollection.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 11%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-disp.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/ReadItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ReadItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Building index for all the packages and classes... [ 11%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadCollectionItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadCollectionItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Standard Doclet version 17.0.11+9-Debian-1 Building tree for all the packages and classes... [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o -MF CMakeFiles/ngs.dir/NGS_Refcount.c.o.d -o CMakeFiles/ngs.dir/NGS_Refcount.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Refcount.c [ 11%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReferenceSequenceItf.cpp [ 11%] Building C object libs/loader/CMakeFiles/loader.dir/reference-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/reference-writer.c.o -MF CMakeFiles/loader.dir/reference-writer.c.o.d -o CMakeFiles/loader.dir/reference-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/reference-writer.c [ 11%] Building C object libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/loader/CMakeFiles/loader.dir/sequence-writer.c.o -MF CMakeFiles/loader.dir/sequence-writer.c.o.d -o CMakeFiles/loader.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/loader/sequence-writer.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 11%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Alignment.html... [ 11%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o -MF CMakeFiles/ngs.dir/NGS_String.c.o.d -o CMakeFiles/ngs.dir/NGS_String.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_String.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadGroupIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 12%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o -MF CMakeFiles/ngs.dir/NGS_Id.c.o.d -o CMakeFiles/ngs.dir/NGS_Id.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_Id.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:217: warning: @return has already been specified * @return '-' if negative strand is transcribed ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:218: warning: @return has already been specified * @return '?' if unknown ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:140: warning: no comment static int all = primaryAlignment | secondaryAlignment; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:176: warning: no comment static int clipLeft = 0; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:177: warning: no comment static int clipRight = 1; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:132: warning: no comment static int maxMapQuality = 8; // pass alignments with mappingQuality <= param ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:131: warning: no comment static int minMapQuality = 4; // pass alignments with mappingQuality >= param ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:133: warning: no comment static int noWraparound = 16; // do not include leading wrapped around alignments to circular references ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:130: warning: no comment static int passDuplicates = 2; // either a PCR or optical duplicate ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:129: warning: no comment static int passFailed = 1; // reads rejected due to platform/vendor quality criteria ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:138: warning: no comment static int primaryAlignment = 1; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:139: warning: no comment static int secondaryAlignment = 2; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Alignment.java:134: warning: no comment static int startWithinSlice = 32; // change slice intersection criteria so that start pos is within slice ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::ReadItf; C = NGS_Read_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::ReadItf; C = NGS_Read_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -MF CMakeFiles/ngs.dir/NGS_ErrBlock.c.o.d -o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ErrBlock.c [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/AlignmentItf.cpp [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlob.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReadIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o [ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_FragmentBlobIterator.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp [ 13%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupIteratorItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/FragmentBlob.cpp [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadGroupItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp [ 13%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/AlignmentIterator.html... In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ErrorMsg.html... [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlob.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:49: warning: no comment public ErrorMsg () ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:53: warning: no comment public ErrorMsg ( String message ) ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ErrorMsg.java:58: warning: no comment public ErrorMsg ( ErrorMsg obj ) ^ [ 13%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -MF CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o.d -o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/NGS_ReferenceBlobIterator.c Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Fragment.html... [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/FragmentItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StatisticsItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Linking CXX static library ../../../../ilib/libngs-bind-c++.a In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReferenceSequenceItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_ReferenceSequenceItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -P CMakeFiles/ngs-bind-c++.dir/cmake_clean_target.cmake Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/FragmentIterator.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html... cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-c++.dir/link.txt --verbose=1 /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:29: warning: no comment public class LibDependencies { ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:34: warning: no comment public final static String NCBI_VDB = "ncbi-ngs"; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/LibDependencies.java:30: warning: no comment public final static String NGS_SDK = "ngs-sdk"; ^ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/AlignmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Reference.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReference.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbReference.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /usr/bin/ar qc ../../../../ilib/libngs-bind-c++.a "CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html... /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:40: warning: no comment public class NGS ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/gov/nih/nlm/ncbi/ngs/NGS.java:133: warning: no comment public static void main(String[] args) { ^ /usr/bin/ranlib ../../../../ilib/libngs-bind-c++.a [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Package.html... make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Pileup.html... [ 13%] Built target ngs-bind-c++ make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/depend [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp [ 13%] Building CXX object ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-py -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -MF CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o.d -o CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StringItf.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/DependInfo.cmake "--color=" [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ReadItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEvent.html... make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build.make libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 13%] Building C object ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o -MF CMakeFiles/ngs.dir/VByteBlob.c.o.d -o CMakeFiles/ngs.dir/VByteBlob.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs/VByteBlob.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StringItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 13%] Building CXX object libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -MF CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o.d -o CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_makedb.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_StatisticsItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/python/py_Refcount.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:118: warning: no comment static int alignment_minus_strand = 0x20; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:116: warning: no comment static int alignment_start = 0x80; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:117: warning: no comment static int alignment_stop = 0x40; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:98: warning: no comment static int deletion = 2; ^ [ 13%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -MF CMakeFiles/ngs-disp.dir/PackageItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/PackageItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:104: warning: no comment static int insertion = 0x08; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:112: warning: no comment static int insertion_before_deletion = insertion | deletion; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:107: warning: no comment static int insertion_before_match = insertion | match; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:108: warning: no comment static int insertion_before_mismatch = insertion | mismatch; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:180: warning: no comment static int intron_minus = 2; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:179: warning: no comment static int intron_plus = 1; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:181: warning: no comment static int intron_unknown = 3; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:97: warning: no comment static int mismatch = 1; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:191: warning: no comment static int read_gap = 5; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:186: warning: no comment static int read_overlap = 4; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/PileupEvent.java:113: warning: no comment static int replacement = insertion_before_deletion; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupItf.cpp:38:7: warning: 'jlong Cast(ngs::PileupEventItf*)' defined but not used [-Wunused-function] 38 | jlong Cast ( PileupEventItf * obj ) | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StatisticsItf; C = NGS_Statistics_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupEventIterator.html... In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PackageItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/PackageItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/PileupIterator.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Read.html... /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:35: warning: no comment [ 13%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/FragmentItf.cpp public interface Read ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:79: warning: no comment static int aligned = fullyAligned | partiallyAligned; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:81: warning: no comment static int all = aligned | unaligned; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:78: warning: no comment static int partiallyAligned = 2; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Read.java:80: warning: no comment static int unaligned = 4; ^ [ 14%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StatisticsItf.cpp [ 14%] Linking C static library ../../../ilib/libngs.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -P CMakeFiles/ngs.dir/cmake_clean_target.cmake Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadCollection.html... [ 14%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../ilib/libngs.a "CMakeFiles/ngs.dir/NCBI-NGS.c.o" CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o CMakeFiles/ngs.dir/CSRA1_Pileup.c.o CMakeFiles/ngs.dir/CSRA1_Alignment.c.o CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o CMakeFiles/ngs.dir/CSRA1_Reference.c.o CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o CMakeFiles/ngs.dir/CSRA1_Read.c.o CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o CMakeFiles/ngs.dir/SRA_Statistics.c.o CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_Read.c.o CMakeFiles/ngs.dir/SRA_ReadGroup.c.o CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o CMakeFiles/ngs.dir/SRA_ReadCollection.c.o CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Statistics.c.o CMakeFiles/ngs.dir/NGS_ReadCollection.c.o CMakeFiles/ngs.dir/NGS_PileupEvent.c.o CMakeFiles/ngs.dir/NGS_Pileup.c.o CMakeFiles/ngs.dir/NGS_ReadGroup.c.o CMakeFiles/ngs.dir/NGS_Alignment.c.o CMakeFiles/ngs.dir/NGS_Reference.c.o CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o CMakeFiles/ngs.dir/NGS_Read.c.o CMakeFiles/ngs.dir/NGS_Fragment.c.o CMakeFiles/ngs.dir/NGS_Cursor.c.o CMakeFiles/ngs.dir/NGS_Refcount.c.o CMakeFiles/ngs.dir/NGS_String.c.o CMakeFiles/ngs.dir/NGS_Id.c.o CMakeFiles/ngs.dir/NGS_ErrBlock.c.o CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o CMakeFiles/ngs.dir/VByteBlob.c.o In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventIteratorItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroup.html... [ 14%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o -MF CMakeFiles/ngs-disp.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-disp.dir/StringItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadGroupIterator.html... /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'C* ngs::Refcount::Test() [with T = ngs::FragmentItf; C = NGS_Fragment_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:100:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this == 0 ) | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReadIterator.html... /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/ReadIterator.java:34: warning: no comment public interface ReadIterator ^ Note: ngs/itf/Refcount.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Reference.html... /usr/bin/ranlib ../../../ilib/libngs.a [ 14%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/StringItf.cpp [ 14%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o -MF CMakeFiles/ngs-disp.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-disp.dir/Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -E touch /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir/java_compiled_ngs-java Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceIterator.html... In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 14%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/ReferenceSequence.html... cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o -MF CMakeFiles/ngs-disp.dir/VTable.cpp.o.d -o CMakeFiles/ngs-disp.dir/VTable.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/VTable.cpp [ 14%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp [ 14%] Generating CMakeFiles/ngs-java.dir/java_class_filelist cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClassFilelist.cmake Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/Statistics.html... /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:41: warning: no comment static int int64 = 2; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:43: warning: no comment static int real = 4; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:40: warning: no comment static int string = 1; ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/ngs/Statistics.java:42: warning: no comment static int uint64 = 3; ^ Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html... In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/PileupEventItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_PileupEventItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 14%] Creating Java archive ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/jar -cf /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar @java_class_filelist Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-summary.html... [ 14%] Built target ngs make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp/CMakeFiles/ascp.dir/DependInfo.cmake "--color=" Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/ngs/package-tree.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/constant-values.html... make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ascp/CMakeFiles/ascp.dir/build.make libs/ascp/CMakeFiles/ascp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 14%] Building C object libs/ascp/CMakeFiles/ascp.dir/ascp.c.o Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/serialized-form.html... cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/ascp/CMakeFiles/ascp.dir/ascp.c.o -MF CMakeFiles/ascp.dir/ascp.c.o.d -o CMakeFiles/ascp.dir/ascp.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp/ascp.c Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-tree.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index.html... [ 14%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlob.cpp [ 14%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -MF CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o.d -o CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/ReferenceBlobIterator.cpp [ 15%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp Building index for all classes... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allclasses-index.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/allpackages-index.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/index-all.html... /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'const char* ngs::StringItf::data() const': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:62:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 62 | if ( this != 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp: In member function 'size_t ngs::StringItf::size() const': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/StringItf.cpp:97:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 97 | if ( this != 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp: In member function 'const C* ngs::Refcount::Test() const [with T = ngs::StringItf; C = NGS_String_v1]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:106:13: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 106 | if ( this == 0 ) | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentIteratorItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/overview-summary.html... Generating /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc/help-doc.html... [ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o 46 warnings cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrBlock.cpp [ 16%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/Refcount.cpp [ 16%] Linking CXX static library ../../../../ilib/libngs-bind-python.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -P CMakeFiles/ngs-bind-python.dir/cmake_clean_target.cmake /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void ngs::OpaqueRefcount::Release()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:69:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 69 | if ( this != 0 ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp: In member function 'void* ngs::OpaqueRefcount::Duplicate() const': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/Refcount.cpp:100:9: warning: 'nonnull' argument 'this' compared to NULL [-Wnonnull-compare] 100 | if ( this != 0 ) | ^~ [ 16%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.29/Modules/UseJava/Symlinks.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/python && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-python.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../ilib/libngs-bind-python.a "CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_AlignmentItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 16%] Building CXX object ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/dispatch/ErrorMsg.cpp [ 16%] Built target ngs-java make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ranlib ../../../../ilib/libngs-bind-python.a make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/diagnose /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose/CMakeFiles/diagnose.dir/DependInfo.cmake "--color=" [ 16%] Built target ngs-doc_javadoc make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/depend [ 16%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/general-writer.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrorMsg.cpp make -f libs/diagnose/CMakeFiles/diagnose.dir/build.make libs/diagnose/CMakeFiles/diagnose.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 16%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/CMakeFiles/general-writer.dir/build.make libs/general-writer/CMakeFiles/general-writer.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 16%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupIteratorItf.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 16%] Built target ngs-bind-python cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/diagnose.c.o -MF CMakeFiles/diagnose.dir/diagnose.c.o.d -o CMakeFiles/diagnose.dir/diagnose.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/diagnose/diagnose.c make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/depend [ 17%] Building CXX object libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/general-writer.cpp.o -MF CMakeFiles/general-writer.dir/general-writer.cpp.o.d -o CMakeFiles/general-writer.dir/general-writer.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 18%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -MF CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o.d -o CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbAlignment.cpp [ 18%] Building CXX object tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -MF CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o.d -o CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_cpp.cpp [ 18%] Building C object libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/ascp/CMakeFiles/ascp.dir/unix/connect.c.o -MF CMakeFiles/ascp.dir/unix/connect.c.o.d -o CMakeFiles/ascp.dir/unix/connect.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c [ 18%] Building C object libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/diagnose -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/diagnose/CMakeFiles/diagnose.dir/endpoint.c.o -MF CMakeFiles/diagnose.dir/endpoint.c.o.d -o CMakeFiles/diagnose.dir/endpoint.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/diagnose/endpoint.c [ 18%] Building CXX object libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT libs/ngs-vdb/CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -MF CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o.d -o CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/NGS-VDB.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Alignment.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbAlignment.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/VdbAlignment.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c: In function 'run_ascp': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:425:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 425 | write(pipeto[1], answer, sizeof y - 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp/unix/connect.c:460:49: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 460 | write(pipeto[1], | ^~~~~~~~~~~~~~~~ 461 | answer, sizeof y - 1); | ~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/adapter/CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -MF CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o.d -o CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/adapter/ErrBlock.cpp [ 18%] Building C object libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/general-writer/CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -MF CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o.d -o CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/utf8-like-int-codec.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/NGS-VDB.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/NGS-VDB.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui/CMakeFiles/tui.dir/DependInfo.cmake "--color=" [ 18%] Building C object libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/ascp\" -Dx86_64 -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/ascp/CMakeFiles/ascp.dir/linux/ascp-path.c.o -MF CMakeFiles/ascp.dir/linux/ascp-path.c.o.d -o CMakeFiles/ascp.dir/linux/ascp-path.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ascp/linux/ascp-path.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/tui/CMakeFiles/tui.dir/build.make tools/external/vdb-config/tui/CMakeFiles/tui.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/dir_dlg.c.o -MF CMakeFiles/tui.dir/dir_dlg.c.o.d -o CMakeFiles/tui.dir/dir_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/dir_dlg.c [ 18%] Linking C static library ../../ilib/libloader.a make -f tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build.make tools/external/sra-dump/CMakeFiles/fastq-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/fastq-dump.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -P CMakeFiles/loader.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/loader.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build.make tools/external/sra-dump/CMakeFiles/fastq-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 18%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/eventring.c.o -MF CMakeFiles/tui.dir/eventring.c.o.d -o CMakeFiles/tui.dir/eventring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/eventring.c /usr/bin/ar qc ../../ilib/libloader.a CMakeFiles/loader.dir/progressbar.c.o "CMakeFiles/loader.dir/loader-file.c.o" "CMakeFiles/loader.dir/loader-meta.c.o" "CMakeFiles/loader.dir/queue-file.c.o" "CMakeFiles/loader.dir/alignment-writer.c.o" "CMakeFiles/loader.dir/common-reader.c.o" "CMakeFiles/loader.dir/common-writer.c.o" CMakeFiles/loader.dir/mmarray.c.o "CMakeFiles/loader.dir/reference-writer.c.o" "CMakeFiles/loader.dir/sequence-writer.c.o" [ 18%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/factory.c.o -MF CMakeFiles/fastq-dump.dir/factory.c.o.d -o CMakeFiles/fastq-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c /usr/bin/ranlib ../../ilib/libloader.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 18%] Linking CXX executable ../../../test-bin/ngs-makedb cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-makedb.dir/link.txt --verbose=1 [ 18%] Built target loader make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-makedb.dir/ngstest_makedb.cpp.o" -o ../../../test-bin/ngs-makedb -Wl,-Bstatic -lktst -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/sff-dump.dir/DependInfo.cmake "--color=" [ 18%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/sff-dump.dir/build.make tools/external/sra-dump/CMakeFiles/sff-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 18%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/factory.c.o -MF CMakeFiles/sff-dump.dir/factory.c.o.d -o CMakeFiles/sff-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadGroupItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadGroupItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 19%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fasta_dump.c.o cd 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Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/file_dlg.c.o -MF CMakeFiles/tui.dir/file_dlg.c.o.d -o CMakeFiles/tui.dir/file_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/file_dlg.c [ 19%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp [ 19%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp [ 19%] Linking C static library ../../ilib/libascp.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -P CMakeFiles/ascp.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/ReadItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadIteratorItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 19%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/core.c.o -MF CMakeFiles/fastq-dump.dir/core.c.o.d -o CMakeFiles/fastq-dump.dir/core.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/line_policy.c.o -MF CMakeFiles/tui.dir/line_policy.c.o.d -o CMakeFiles/tui.dir/line_policy.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/line_policy.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ascp && /usr/bin/cmake -E cmake_link_script CMakeFiles/ascp.dir/link.txt --verbose=1 In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ReadItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /usr/bin/ar qc ../../ilib/libascp.a CMakeFiles/ascp.dir/ascp.c.o CMakeFiles/ascp.dir/unix/connect.c.o "CMakeFiles/ascp.dir/linux/ascp-path.c.o" /usr/bin/ranlib ../../ilib/libascp.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Built target ascp make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/illumina-dump.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build.make tools/external/sra-dump/CMakeFiles/illumina-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 19%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/factory.c.o -MF CMakeFiles/illumina-dump.dir/factory.c.o.d -o CMakeFiles/illumina-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c [ 19%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/screen.c.o -MF CMakeFiles/tui.dir/screen.c.o.d -o CMakeFiles/tui.dir/screen.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/screen.c [ 19%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp [ 19%] Linking CXX static library ../../../ilib/libngs-disp.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -P CMakeFiles/ngs-disp.dir/cmake_clean_target.cmake [ 19%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/dispatch && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-disp.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_StatisticsItf.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StatisticsItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_StatisticsItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 20%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/string_cache.c.o -MF CMakeFiles/tui.dir/string_cache.c.o.d -o CMakeFiles/tui.dir/string_cache.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/string_cache.c /usr/bin/ar qc ../../../ilib/libngs-disp.a "CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "CMakeFiles/ngs-disp.dir/VTable.cpp.o" "CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/FragmentItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_FragmentItf.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 20%] Linking CXX static library ../../../ilib/libngs-adapt-c++.a /usr/bin/ranlib ../../../ilib/libngs-disp.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -P CMakeFiles/ngs-adapt-c++.dir/cmake_clean_target.cmake make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 20%] Built target ngs-disp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/adapter && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-adapt-c++.dir/link.txt --verbose=1 [ 20%] Building C object tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/fastq-dump.dir/fastq.c.o -MF CMakeFiles/fastq-dump.dir/fastq.c.o.d -o CMakeFiles/fastq-dump.dir/fastq.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fastq.c [ 20%] Built target ngs-makedb make -f tools/external/sra-dump/CMakeFiles/abi-dump.dir/build.make tools/external/sra-dump/CMakeFiles/abi-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump/CMakeFiles/abi-dump.dir/DependInfo.cmake "--color=" /usr/bin/ar qc ../../../ilib/libngs-adapt-c++.a "CMakeFiles/ngs-adapt-c++.dir/ReadCollectionItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/PileupEventItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/AlignmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadGroupItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ReadItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/FragmentItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StatisticsItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/StringItf.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/Refcount.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrorMsg.cpp.o" "CMakeFiles/ngs-adapt-c++.dir/ErrBlock.cpp.o" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-dump/CMakeFiles/abi-dump.dir/build.make tools/external/sra-dump/CMakeFiles/abi-dump.dir/build /usr/bin/ranlib ../../../ilib/libngs-adapt-c++.a make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 20%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/factory.c.o -MF CMakeFiles/abi-dump.dir/factory.c.o.d -o CMakeFiles/abi-dump.dir/factory.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/factory.c [ 20%] Built target ngs-adapt-c++ make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build.make tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 20%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/fasta_dump.c.o -MF CMakeFiles/abi-dump.dir/fasta_dump.c.o.d -o CMakeFiles/abi-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c [ 20%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/dyn_string.c.o -MF CMakeFiles/sra-pileup.dir/dyn_string.c.o.d -o CMakeFiles/sra-pileup.dir/dyn_string.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c [ 20%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/core.c.o -MF CMakeFiles/abi-dump.dir/core.c.o.d -o CMakeFiles/abi-dump.dir/core.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c [ 20%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui.c.o -MF CMakeFiles/tui.dir/tui.c.o.d -o CMakeFiles/tui.dir/tui.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui.c [ 20%] Linking CXX static library ../../ilib/libngs-vdb.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -P CMakeFiles/ngs-vdb.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-vdb.dir/link.txt --verbose=1 [ 21%] Building C object tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/abi-dump.dir/abi.c.o -MF CMakeFiles/abi-dump.dir/abi.c.o.d -o CMakeFiles/abi-dump.dir/abi.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/abi.c /usr/bin/ar qc ../../ilib/libngs-vdb.a "CMakeFiles/ngs-vdb.dir/VdbReadCollection.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/FragmentBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbReference.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlob.cpp.o" "CMakeFiles/ngs-vdb.dir/ReferenceBlobIterator.cpp.o" "CMakeFiles/ngs-vdb.dir/VdbAlignment.cpp.o" "CMakeFiles/ngs-vdb.dir/NGS-VDB.cpp.o" /usr/bin/ranlib ../../ilib/libngs-vdb.a /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = short unsigned int; uint8_t = unsigned char]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:646:17: warning: unused variable 'ret2' [-Wunused-variable] 646 | int ret2 = decode_uint16 ( start, start + ret, & val2 ); | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = unsigned int; uint8_t = unsigned char]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:659:17: warning: unused variable 'ret2' [-Wunused-variable] 659 | int ret2 = decode_uint32 ( start, start + ret, & val2 ); | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp: In function 'int ncbi::encode_int(T, uint8_t*, uint8_t*) [with T = long unsigned int; uint8_t = unsigned char]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/general-writer.cpp:672:17: warning: unused variable 'ret2' [-Wunused-variable] 672 | int ret2 = decode_uint64 ( start, start + ret, & val2 ); | ^~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Built target ngs-vdb make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup/CMakeFiles/sam-dump.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build.make tools/external/sra-pileup/CMakeFiles/sam-dump.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Linking CXX static library ../../../../ilib/libtui_cpp.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui_cpp.dir/cmake_clean_target.cmake [ 21%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/inputfiles.c.o -MF CMakeFiles/sam-dump.dir/inputfiles.c.o.d -o CMakeFiles/sam-dump.dir/inputfiles.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/inputfiles.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui_cpp.dir/link.txt --verbose=1 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 21%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg.c.o -MF CMakeFiles/tui.dir/tui_dlg.c.o.d -o CMakeFiles/tui.dir/tui_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg.c /usr/bin/ar qc ../../../../ilib/libtui_cpp.a CMakeFiles/tui_cpp.dir/tui_cpp.cpp.o [ 21%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/fasta_dump.c.o -MF CMakeFiles/sff-dump.dir/fasta_dump.c.o.d -o CMakeFiles/sff-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c /usr/bin/ranlib ../../../../ilib/libtui_cpp.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Built target tui_cpp make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build.make tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/build [ 21%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o [ 21%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o -MF CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o.d -o CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_dlg_helper.c.o -MF CMakeFiles/tui.dir/tui_dlg_helper.c.o.d -o CMakeFiles/tui.dir/tui_dlg_helper.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_dlg_helper.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 21%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp [ 22%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/helper.c.o -MF CMakeFiles/fasterq-dump.dir/helper.c.o.d -o CMakeFiles/fasterq-dump.dir/helper.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/helper.c [ 22%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/arg_helper.c.o -MF CMakeFiles/fasterq-dump.dir/arg_helper.c.o.d -o CMakeFiles/fasterq-dump.dir/arg_helper.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/arg_helper.c [ 22%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_menu.c.o -MF CMakeFiles/tui.dir/tui_menu.c.o.d -o CMakeFiles/tui.dir/tui_menu.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c [ 23%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Package.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_String.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 23%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/perf_log.c.o -MF CMakeFiles/sam-dump.dir/perf_log.c.o.d -o CMakeFiles/sam-dump.dir/perf_log.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/perf_log.c [ 23%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -MF CMakeFiles/fasterq-dump.dir/dflt_defline.c.o.d -o CMakeFiles/fasterq-dump.dir/dflt_defline.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/dflt_defline.c [ 23%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o [ 23%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -MF CMakeFiles/fasterq-dump.dir/tool_ctx.c.o.d -o CMakeFiles/fasterq-dump.dir/tool_ctx.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tool_ctx.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_palette.c.o -MF CMakeFiles/tui.dir/tui_palette.c.o.d -o CMakeFiles/tui.dir/tui_palette.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_palette.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c: In function 'foreach_argument': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:443:20: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 443 | if ( rc == 0 && path != NULL ) { | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cmdline_cmn.c:394:10: note: 'rc' was declared here 394 | rc_t rc; | ^~ [ 23%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/fasta_dump.c.o -MF CMakeFiles/illumina-dump.dir/fasta_dump.c.o.d -o CMakeFiles/illumina-dump.dir/fasta_dump.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/fasta_dump.c [ 23%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_std_dlg.c.o -MF CMakeFiles/tui.dir/tui_std_dlg.c.o.d -o CMakeFiles/tui.dir/tui_std_dlg.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_std_dlg.c [ 23%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/inspector.c.o -MF CMakeFiles/fasterq-dump.dir/inspector.c.o.d -o CMakeFiles/fasterq-dump.dir/inspector.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/inspector.c [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/rna_splice_log.c.o -MF CMakeFiles/sam-dump.dir/rna_splice_log.c.o.d -o CMakeFiles/sam-dump.dir/rna_splice_log.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/rna_splice_log.c [ 24%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/out_redir.c.o -MF CMakeFiles/sra-pileup.dir/out_redir.c.o.d -o CMakeFiles/sra-pileup.dir/out_redir.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c: In function 'KTUI_Menu_Remove_Id': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c:408:22: warning: 'idx' may be used uninitialized [-Wmaybe-uninitialized] 408 | rc = VectorRemove ( &parent->children, idx, &removed ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_menu.c:401:22: note: 'idx' was declared here 401 | uint32_t idx; | ^~~ [ 24%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sbuffer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. 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-Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/var_fmt.c.o -MF CMakeFiles/fasterq-dump.dir/var_fmt.c.o.d -o CMakeFiles/fasterq-dump.dir/var_fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/var_fmt.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 27%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_button.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb 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object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/reref.c.o -MF CMakeFiles/sra-pileup.dir/reref.c.o.d -o CMakeFiles/sra-pileup.dir/reref.c.o -c 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-std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/flex_printer.c.o -MF CMakeFiles/fasterq-dump.dir/flex_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/flex_printer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/flex_printer.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_Refcount.cpp:30: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 27%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_dir.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb 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-DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_checkbox.c.o -MF CMakeFiles/tui.dir/tui_widget_checkbox.c.o.d -o CMakeFiles/tui.dir/tui_widget_checkbox.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_checkbox.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/core.c:1010:23: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1010 | ReportBuildDate ( __DATE__ ); | ^~~~~~~~ [ 27%] Building CXX object ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-jni -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ngs-sdk/language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -MF CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o.d -o CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/language/java/jni_ErrorMsg.cpp [ 27%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_grid.c.o -MF CMakeFiles/tui.dir/tui_widget_grid.c.o.d -o CMakeFiles/tui.dir/tui_widget_grid.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_grid.c [ 27%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/progress_thread.c.o -MF CMakeFiles/fasterq-dump.dir/progress_thread.c.o.d -o CMakeFiles/fasterq-dump.dir/progress_thread.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/progress_thread.c [ 27%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cleanup_task.c.o -MF CMakeFiles/fasterq-dump.dir/cleanup_task.c.o.d -o CMakeFiles/fasterq-dump.dir/cleanup_task.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cleanup_task.c [ 27%] Linking C executable ../../../bin/abi-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-dump.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-dump.dir/factory.c.o" "CMakeFiles/abi-dump.dir/fasta_dump.c.o" "CMakeFiles/abi-dump.dir/core.c.o" "CMakeFiles/abi-dump.dir/abi.c.o" -o ../../../bin/abi-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 27%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/cg_tools.c.o cd 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Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/index.c.o -MF CMakeFiles/fasterq-dump.dir/index.c.o.d -o CMakeFiles/fasterq-dump.dir/index.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/index.c [ 27%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_writer.c.o -MF CMakeFiles/fasterq-dump.dir/lookup_writer.c.o.d -o CMakeFiles/fasterq-dump.dir/lookup_writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/lookup_writer.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'fmt_cigar_elem': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:491:10: warning: unused variable 'rc' [-Wunused-variable] 491 | rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); | ^~ [ 27%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/lookup_reader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-dump abi-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3.0.3 abi-dump.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-dump.3 abi-dump make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 28%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_file_list.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/report_deletes.c.o -MF CMakeFiles/sra-pileup.dir/report_deletes.c.o.d -o CMakeFiles/sra-pileup.dir/report_deletes.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/report_deletes.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-context.c [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/locked_value.c.o -MF CMakeFiles/fasterq-dump.dir/locked_value.c.o.d -o CMakeFiles/fasterq-dump.dir/locked_value.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/locked_value.c [ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_label.c.o -MF CMakeFiles/tui.dir/tui_widget_label.c.o.d -o CMakeFiles/tui.dir/tui_widget_label.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_label.c [ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_progress.c.o -MF CMakeFiles/tui.dir/tui_widget_progress.c.o.d -o CMakeFiles/tui.dir/tui_widget_progress.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_progress.c [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_printer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/file_printer.c.o -MF CMakeFiles/fasterq-dump.dir/file_printer.c.o.d -o CMakeFiles/fasterq-dump.dir/file_printer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/file_printer.c [ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_radiobox.c.o cd 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-c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_radiobox.c [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -MF CMakeFiles/fasterq-dump.dir/merge_sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/merge_sorter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/merge_sorter.c [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/sorter.c.o -MF CMakeFiles/fasterq-dump.dir/sorter.c.o.d -o CMakeFiles/fasterq-dump.dir/sorter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/sorter.c [ 29%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -MF CMakeFiles/fasterq-dump.dir/cmn_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/cmn_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/cmn_iter.c [ 29%] Linking CXX static library ../../../../ilib/libngs-bind-java.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -P CMakeFiles/ngs-bind-java.dir/cmake_clean_target.cmake [ 29%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_regions.c.o -MF CMakeFiles/sra-pileup.dir/ref_regions.c.o.d -o CMakeFiles/sra-pileup.dir/ref_regions.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_regions.c [ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_spin_edit.c.o cd 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CMakeFiles/tui.dir/tui_widget_spin_edit.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_spin_edit.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/language/java && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-bind-java.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../../ilib/libngs-bind-java.a "CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" [ 29%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_string_list.c.o -MF CMakeFiles/tui.dir/tui_widget_string_list.c.o.d -o CMakeFiles/tui.dir/tui_widget_string_list.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_string_list.c [ 30%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/tui_widget_tabhdr.c.o -MF CMakeFiles/tui.dir/tui_widget_tabhdr.c.o.d -o CMakeFiles/tui.dir/tui_widget_tabhdr.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/tui_widget_tabhdr.c [ 30%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o -MF CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/raw_read_iter.c /usr/bin/ranlib ../../../../ilib/libngs-bind-java.a [ 30%] Building C object tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"libs/tui\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/.. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/tui/CMakeFiles/tui.dir/linux/systui.c.o -MF CMakeFiles/tui.dir/linux/systui.c.o.d -o CMakeFiles/tui.dir/linux/systui.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/tui/linux/systui.c [ 30%] Building C object tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/illumina-dump.dir/illumina.c.o -MF CMakeFiles/illumina-dump.dir/illumina.c.o.d -o CMakeFiles/illumina-dump.dir/illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/illumina.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 30%] Built target ngs-bind-java make -f tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/DependInfo.cmake "--color=" [ 30%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/4na_ascii.c.o -MF CMakeFiles/sra-pileup.dir/4na_ascii.c.o.d -o CMakeFiles/sra-pileup.dir/4na_ascii.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/4na_ascii.c [ 30%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/special_iter.c.o -MF CMakeFiles/fasterq-dump.dir/special_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/special_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/special_iter.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build.make tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1563:25: warning: 'total_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1563 | KOutMsg( "%d%c", total_cnt,op ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here 1549 | int i, total_cnt, cnt; | ^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 1579 | return rc; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1547:10: note: 'rc' was declared here 1547 | rc_t rc; | ^~ [ 30%] Building C object tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-validate/CMakeFiles/vdb-validate.dir/vdb-validate.c.o -MF CMakeFiles/vdb-validate.dir/vdb-validate.c.o.d -o CMakeFiles/vdb-validate.dir/vdb-validate.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c [ 31%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-coldefs.c [ 31%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o [ 31%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fastq_iter.c.o -MF CMakeFiles/fasterq-dump.dir/fastq_iter.c.o.d -o CMakeFiles/fasterq-dump.dir/fastq_iter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/fastq_iter.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker_0.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker_0.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker_0.c [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/db_join.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/db_join.c.o -MF CMakeFiles/fasterq-dump.dir/db_join.c.o.d -o CMakeFiles/fasterq-dump.dir/db_join.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/db_join.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/ref_walker.c.o -MF CMakeFiles/sra-pileup.dir/ref_walker.c.o.d -o CMakeFiles/sra-pileup.dir/ref_walker.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c [ 32%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-tools.c [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/tbl_join.c.o cd 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/tbl_join.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/out_redir.c.o -MF CMakeFiles/sam-dump.dir/out_redir.c.o.d -o CMakeFiles/sam-dump.dir/out_redir.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/out_redir.c [ 32%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-str.c [ 32%] Building C object tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-dump/CMakeFiles/sff-dump.dir/sff.c.o -MF CMakeFiles/sff-dump.dir/sff.c.o.d -o CMakeFiles/sff-dump.dir/sff.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-dump/sff.c [ 32%] Linking C static library ../../../../ilib/libtui.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -P CMakeFiles/tui.dir/cmake_clean_target.cmake In function 'make_cursor_ids', inlined from 'ref_walker_add_iterator.isra' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:591:15: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:534:14: warning: 'ids' may be used uninitialized [-Wmaybe-uninitialized] 534 | rc = VectorAppend ( cursor_id_vector, NULL, ids ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/ref_walker.c:34: /usr/include/ncbi-vdb/klib/vector.h: In function 'ref_walker_add_iterator.isra': /usr/include/ncbi-vdb/klib/vector.h:401:21: note: by argument 3 of type 'const void *' to 'VectorAppend' declared here 401 | KLIB_EXTERN rc_t CC VectorAppend ( Vector *self, uint32_t *idx, const void *item ); | ^~~~~~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/tui && /usr/bin/cmake -E cmake_link_script CMakeFiles/tui.dir/link.txt --verbose=1 [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/walk_debug.c.o -MF CMakeFiles/sra-pileup.dir/walk_debug.c.o.d -o CMakeFiles/sra-pileup.dir/walk_debug.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/walk_debug.c /usr/bin/ar qc ../../../../ilib/libtui.a CMakeFiles/tui.dir/dir_dlg.c.o CMakeFiles/tui.dir/eventring.c.o CMakeFiles/tui.dir/file_dlg.c.o CMakeFiles/tui.dir/line_policy.c.o CMakeFiles/tui.dir/screen.c.o CMakeFiles/tui.dir/string_cache.c.o CMakeFiles/tui.dir/tui.c.o CMakeFiles/tui.dir/tui_dlg.c.o CMakeFiles/tui.dir/tui_dlg_helper.c.o CMakeFiles/tui.dir/tui_menu.c.o CMakeFiles/tui.dir/tui_palette.c.o CMakeFiles/tui.dir/tui_std_dlg.c.o CMakeFiles/tui.dir/tui_widget.c.o CMakeFiles/tui.dir/tui_widget_button.c.o CMakeFiles/tui.dir/tui_widget_checkbox.c.o CMakeFiles/tui.dir/tui_widget_grid.c.o CMakeFiles/tui.dir/tui_widget_inputline.c.o CMakeFiles/tui.dir/tui_widget_label.c.o CMakeFiles/tui.dir/tui_widget_progress.c.o CMakeFiles/tui.dir/tui_widget_radiobox.c.o CMakeFiles/tui.dir/tui_widget_spin_edit.c.o CMakeFiles/tui.dir/tui_widget_string_list.c.o CMakeFiles/tui.dir/tui_widget_tabhdr.c.o CMakeFiles/tui.dir/linux/systui.c.o [ 32%] Linking CXX static library ../../ilib/libgeneral-writer.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -P CMakeFiles/general-writer.dir/cmake_clean_target.cmake /usr/bin/ranlib ../../../../ilib/libtui.a [ 32%] Linking C executable ../../../bin/illumina-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-dump.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-writer.dir/link.txt --verbose=1 [ 32%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/temp_registry.c.o -MF CMakeFiles/fasterq-dump.dir/temp_registry.c.o.d -o CMakeFiles/fasterq-dump.dir/temp_registry.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/temp_registry.c [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr.c [ 32%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-helper.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-dump.dir/factory.c.o" "CMakeFiles/illumina-dump.dir/fasta_dump.c.o" "CMakeFiles/illumina-dump.dir/core.c.o" "CMakeFiles/illumina-dump.dir/illumina.c.o" -o ../../../bin/illumina-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 32%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o [ 32%] Linking C executable ../../../bin/sff-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_counters.c.o -MF CMakeFiles/sra-pileup.dir/pileup_counters.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_counters.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_counters.c [ 32%] Built target tui make -f tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-dump.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ar qc ../../ilib/libgeneral-writer.a "CMakeFiles/general-writer.dir/general-writer.cpp.o" "CMakeFiles/general-writer.dir/utf8-like-int-codec.c.o" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/DependInfo.cmake "--color=" [ 32%] Linking C executable ../../../bin/fastq-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastq-dump.dir/link.txt --verbose=1 /usr/bin/ranlib ../../ilib/libgeneral-writer.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build.make tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-dump.dir/factory.c.o" "CMakeFiles/sff-dump.dir/fasta_dump.c.o" "CMakeFiles/sff-dump.dir/core.c.o" "CMakeFiles/sff-dump.dir/sff.c.o" -o ../../../bin/sff-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fastq-dump.dir/factory.c.o" "CMakeFiles/fastq-dump.dir/fasta_dump.c.o" "CMakeFiles/fastq-dump.dir/core.c.o" "CMakeFiles/fastq-dump.dir/fastq.c.o" -o ../../../bin/fastq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-dump.3.0.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-dump illumina-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3.0.3 illumina-dump.3 [ 32%] Built target general-writer make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-dump.3 illumina-dump make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/DependInfo.cmake "--color=" [ 33%] Building CXX object tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-validate\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-validate/CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -MF CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o.d -o CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/check-corrupt.cpp [ 33%] Built target illumina-dump make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build.make tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -MF CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o.d -o CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-encrypt.c [ 33%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -MF CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o.d -o CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/vdb-decrypt.c [ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/copy_machine.c.o -MF CMakeFiles/fasterq-dump.dir/copy_machine.c.o.d -o CMakeFiles/fasterq-dump.dir/copy_machine.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/fasterq-dump/copy_machine.c [ 33%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_index.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_index.c.o -MF CMakeFiles/sra-pileup.dir/pileup_index.c.o.d -o CMakeFiles/sra-pileup.dir/pileup_index.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/pileup_index.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-dump.3.0.3 [ 33%] Linking C static library ../../ilib/libdiagnose.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-dump fastq-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3.0.3 fastq-dump.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -P CMakeFiles/diagnose.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-dump.3 fastq-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fastq-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/concatenator.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath/CMakeFiles/srapath.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/diagnose && /usr/bin/cmake -E cmake_link_script CMakeFiles/diagnose.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3.0.3 sff-dump.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-dump.3 sff-dump make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o cd 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-formats.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/srapath/CMakeFiles/srapath.dir/build.make tools/external/srapath/CMakeFiles/srapath.dir/build [ 33%] Built target sff-dump make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 33%] Building C object tools/external/fasterq-dump/CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fasterq-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g 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/build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-stat /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat/CMakeFiles/sra-stat.dir/DependInfo.cmake "--color=" /usr/bin/ranlib ../../ilib/libdiagnose.a [ 33%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o [ 34%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-encrypt.dir/shared.c.o -MF CMakeFiles/vdb-encrypt.dir/shared.c.o.d -o CMakeFiles/vdb-encrypt.dir/shared.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/helper.c.o -MF CMakeFiles/srapath.dir/helper.c.o.d -o CMakeFiles/srapath.dir/helper.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/helper.c [ 34%] Building C object tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-decrypt\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-decrypt/CMakeFiles/vdb-decrypt.dir/shared.c.o -MF CMakeFiles/vdb-decrypt.dir/shared.c.o.d -o CMakeFiles/vdb-decrypt.dir/shared.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-decrypt/shared.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-stat/CMakeFiles/sra-stat.dir/build.make tools/external/sra-stat/CMakeFiles/sra-stat.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/pileup_indels.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD 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-I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/rcexplain/CMakeFiles/rcexplain.dir/rcexplain.c.o -MF CMakeFiles/rcexplain.dir/rcexplain.c.o.d -o CMakeFiles/rcexplain.dir/rcexplain.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/rcexplain/rcexplain.c [ 35%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE 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-fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-hdr1.c.o -MF CMakeFiles/sam-dump.dir/sam-hdr1.c.o.d -o CMakeFiles/sam-dump.dir/sam-hdr1.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-hdr1.c [ 35%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump-fastq.c [ 35%] Linking C executable ../../../bin/rcexplain cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/rcexplain && /usr/bin/cmake -E cmake_link_script CMakeFiles/rcexplain.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/rcexplain.dir/rcexplain.c.o -o 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-fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/repository-mgr.c.o -MF CMakeFiles/srapath.dir/repository-mgr.c.o.d -o CMakeFiles/srapath.dir/repository-mgr.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/repository-mgr.c [ 35%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb_info.c.o -MF CMakeFiles/vdb-dump.dir/vdb_info.c.o.d -o CMakeFiles/vdb-dump.dir/vdb_info.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c: In function 'ric_align_generic.constprop': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c:1393:12: warning: 'last' may be used uninitialized [-Wmaybe-uninitialized] 1393 | if (chunk == last) | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-validate/vdb-validate.c:1384:17: note: 'last' was declared here 1384 | int64_t last; | ^~~~ [ 35%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/services.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/services.c.o -MF CMakeFiles/srapath.dir/services.c.o.d -o CMakeFiles/srapath.dir/services.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c: In function 'json_print_named_url': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c:338:10: warning: unused variable 'rc' [-Wunused-variable] 338 | rc_t rc = VPathMakeString(url, &tmp); assert(rc == 0); | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c: In function 'json_print_named_urls_and_service': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/services.c:356:14: warning: unused variable 'rc' [-Wunused-variable] 356 | rc_t rc = VPathMakeString(url, &tmp); assert(rc == 0); | ^~ [ 35%] Building C object tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-dump/CMakeFiles/vdb-dump.dir/vdb-dump.c.o -MF CMakeFiles/vdb-dump.dir/vdb-dump.c.o.d -o CMakeFiles/vdb-dump.dir/vdb-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb-dump.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rcexplain.3.0.3 [ 35%] Building C object libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o [ 35%] Building C object tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sra-pileup.dir/sra-pileup.c.o -MF CMakeFiles/sra-pileup.dir/sra-pileup.c.o.d -o CMakeFiles/sra-pileup.dir/sra-pileup.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rcexplain rcexplain.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__mod__=\"libs/vdb-sqlite\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -fPIC -rdynamic -Wall -MD -MT libs/vdb-sqlite/CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -MF CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o.d -o CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3vdb.c [ 35%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/cgi_request.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/cgi_request.c.o -MF CMakeFiles/srapath.dir/cgi_request.c.o.d -o CMakeFiles/srapath.dir/cgi_request.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/cgi_request.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3.0.3 rcexplain.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rcexplain.3 rcexplain make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Building C object tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-stat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-stat/CMakeFiles/sra-stat.dir/sra-stat.c.o -MF CMakeFiles/sra-stat.dir/sra-stat.c.o.d -o CMakeFiles/sra-stat.dir/sra-stat.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-stat/sra-stat.c [ 35%] Built target rcexplain make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/depend [ 35%] Building C object tools/external/srapath/CMakeFiles/srapath.dir/srapath.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/srapath\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/srapath/CMakeFiles/srapath.dir/srapath.c.o -MF CMakeFiles/srapath.dir/srapath.c.o.d -o CMakeFiles/srapath.dir/srapath.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/srapath/srapath.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build.make tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Building C object tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/util\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/kdbmeta/CMakeFiles/kdbmeta.dir/kdbmeta.c.o -MF CMakeFiles/kdbmeta.dir/kdbmeta.c.o.d -o CMakeFiles/kdbmeta.dir/kdbmeta.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/kdbmeta/kdbmeta.c [ 35%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/matecache.c.o -MF CMakeFiles/sam-dump.dir/matecache.c.o.d -o CMakeFiles/sam-dump.dir/matecache.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/matecache.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sra-pileup.c:1415:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1415 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ [ 35%] Linking C executable ../../../bin/vdb-decrypt cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-decrypt.dir/link.txt --verbose=1 [ 35%] Linking C executable ../../../bin/vdb-encrypt cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-decrypt && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-encrypt.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-decrypt.dir/vdb-decrypt.c.o" "CMakeFiles/vdb-decrypt.dir/shared.c.o" -o ../../../bin/vdb-decrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-encrypt.dir/vdb-encrypt.c.o" "CMakeFiles/vdb-encrypt.dir/shared.c.o" -o ../../../bin/vdb-encrypt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-encrypt.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-encrypt vdb-encrypt.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3.0.3 vdb-encrypt.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-encrypt.3 vdb-encrypt make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Built target vdb-encrypt make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/align-info /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info/CMakeFiles/align-info.dir/DependInfo.cmake "--color=" [ 35%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/read_fkt.c.o -MF CMakeFiles/sam-dump.dir/read_fkt.c.o.d -o CMakeFiles/sam-dump.dir/read_fkt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/read_fkt.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/align-info/CMakeFiles/align-info.dir/build.make tools/external/align-info/CMakeFiles/align-info.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-aligned.c.o -MF CMakeFiles/sam-dump.dir/sam-aligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-aligned.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-aligned.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-decrypt.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-decrypt vdb-decrypt.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3.0.3 vdb-decrypt.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-decrypt.3 vdb-decrypt [ 35%] Building C object tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/align-info\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/align-info/CMakeFiles/align-info.dir/align-info.c.o -MF CMakeFiles/align-info.dir/align-info.c.o.d -o CMakeFiles/align-info.dir/align-info.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/align-info/align-info.c In function 'inspect_line', inlined from 'parse_buffer' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:602:29, inlined from 'get_meta_bam_hdr' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:639:21, inlined from 'get_meta_info' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:681:5: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:568:38: warning: 'line' may be used uninitialized [-Wmaybe-uninitialized] 568 | if ( ( len > 3 ) && ( '@' == line[ 0 ] ) ) | ~~~~^~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c: In function 'get_meta_info': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-dump/vdb_info.c:582:12: note: 'line' was declared here 582 | char * line; | ^~~~ [ 35%] Built target vdb-decrypt make -f tools/external/test-sra/CMakeFiles/test-sra.dir/build.make tools/external/test-sra/CMakeFiles/test-sra.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/test-sra /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra/CMakeFiles/test-sra.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/test-sra/CMakeFiles/test-sra.dir/build.make tools/external/test-sra/CMakeFiles/test-sra.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 35%] Building C object tools/external/test-sra/CMakeFiles/test-sra.dir/test-sra.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/test-sra\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/test-sra/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/test-sra/CMakeFiles/test-sra.dir/test-sra.c.o -MF CMakeFiles/test-sra.dir/test-sra.c.o.d -o CMakeFiles/test-sra.dir/test-sra.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/test-sra/test-sra.c [ 36%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-unaligned.c.o -MF CMakeFiles/sam-dump.dir/sam-unaligned.c.o.d -o CMakeFiles/sam-dump.dir/sam-unaligned.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c make -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build.make tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 37%] Building C object tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cache-mgr\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/cache-mgr/CMakeFiles/cache-mgr.dir/cache-mgr.c.o -MF CMakeFiles/cache-mgr.dir/cache-mgr.c.o.d -o CMakeFiles/cache-mgr.dir/cache-mgr.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c [ 37%] Linking C executable ../../../bin/fasterq-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/fasterq-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/fasterq-dump.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fasterq-dump.dir/helper.c.o" "CMakeFiles/fasterq-dump.dir/arg_helper.c.o" "CMakeFiles/fasterq-dump.dir/dflt_defline.c.o" "CMakeFiles/fasterq-dump.dir/tool_ctx.c.o" "CMakeFiles/fasterq-dump.dir/inspector.c.o" "CMakeFiles/fasterq-dump.dir/sbuffer.c.o" "CMakeFiles/fasterq-dump.dir/err_msg.c.o" "CMakeFiles/fasterq-dump.dir/file_tools.c.o" "CMakeFiles/fasterq-dump.dir/var_fmt.c.o" "CMakeFiles/fasterq-dump.dir/flex_printer.c.o" "CMakeFiles/fasterq-dump.dir/temp_dir.c.o" "CMakeFiles/fasterq-dump.dir/progress_thread.c.o" "CMakeFiles/fasterq-dump.dir/cleanup_task.c.o" "CMakeFiles/fasterq-dump.dir/index.c.o" "CMakeFiles/fasterq-dump.dir/lookup_writer.c.o" "CMakeFiles/fasterq-dump.dir/lookup_reader.c.o" "CMakeFiles/fasterq-dump.dir/locked_file_list.c.o" "CMakeFiles/fasterq-dump.dir/locked_value.c.o" "CMakeFiles/fasterq-dump.dir/file_printer.c.o" "CMakeFiles/fasterq-dump.dir/merge_sorter.c.o" "CMakeFiles/fasterq-dump.dir/sorter.c.o" "CMakeFiles/fasterq-dump.dir/cmn_iter.c.o" "CMakeFiles/fasterq-dump.dir/raw_read_iter.c.o" "CMakeFiles/fasterq-dump.dir/special_iter.c.o" "CMakeFiles/fasterq-dump.dir/fastq_iter.c.o" "CMakeFiles/fasterq-dump.dir/db_join.c.o" "CMakeFiles/fasterq-dump.dir/tbl_join.c.o" "CMakeFiles/fasterq-dump.dir/temp_registry.c.o" "CMakeFiles/fasterq-dump.dir/copy_machine.c.o" "CMakeFiles/fasterq-dump.dir/concatenator.c.o" "CMakeFiles/fasterq-dump.dir/fasterq-dump.c.o" -o ../../../bin/fasterq-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c: In function 'print_sliced_quality': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:407:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 407 | return rc; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-unaligned.c:391:10: note: 'rc' was declared here 391 | rc_t rc; | ^~ make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool/CMakeFiles/sratools.dir/DependInfo.cmake "--color=" [ 37%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/md_flag.c.o -MF CMakeFiles/sam-dump.dir/md_flag.c.o.d -o CMakeFiles/sam-dump.dir/md_flag.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/md_flag.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/driver-tool/CMakeFiles/sratools.dir/build.make tools/external/driver-tool/CMakeFiles/sratools.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fasterq-dump.3.0.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fasterq-dump fasterq-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3.0.3 fasterq-dump.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fasterq-dump.3 fasterq-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 fasterq-dump-driver /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c: In function 'perform_report': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:702:16: warning: storing the address of local variable 'data' in '*octx.data' [-Wdangling-pointer=] 702 | octx->data = &data; | ~~~~~~~~~~~^~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:699:17: note: 'data' declared here 699 | report_data data; | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:696:41: note: 'octx' declared here 696 | static rc_t perform_report( visit_ctx * octx ) | ~~~~~~~~~~~~^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c: In function 'perform_unlock': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:905:16: warning: storing the address of local variable 'data' in '*octx.data' [-Wdangling-pointer=] 905 | octx->data = &data; | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:902:17: note: 'data' declared here 902 | unlock_data data; | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:899:41: note: 'octx' declared here 899 | static rc_t perform_unlock( visit_ctx * octx ) | ~~~~~~~~~~~~^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c: In function 'perform_clear': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:990:16: warning: storing the address of local variable 'data' in '*octx.data' [-Wdangling-pointer=] 990 | octx->data = &data; | ~~~~~~~~~~~^~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:987:16: note: 'data' declared here 987 | clear_data data; | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/cache-mgr/cache-mgr.c:984:40: note: 'octx' declared here 984 | static rc_t perform_clear( visit_ctx * octx ) | ~~~~~~~~~~~~^~~~ [ 37%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/sratools.cpp.o -MF CMakeFiles/sratools.dir/sratools.cpp.o.d -o CMakeFiles/sratools.dir/sratools.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp [ 37%] Linking C executable ../../../bin/srapath cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/srapath && /usr/bin/cmake -E cmake_link_script CMakeFiles/srapath.dir/link.txt --verbose=1 [ 37%] Built target fasterq-dump make -f tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build.make tools/loaders/bam-loader/CMakeFiles/bam-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/bam-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build.make tools/loaders/bam-loader/CMakeFiles/bam-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/srapath.dir/helper.c.o CMakeFiles/srapath.dir/line_iter.c.o "CMakeFiles/srapath.dir/repository-mgr.c.o" CMakeFiles/srapath.dir/services.c.o CMakeFiles/srapath.dir/cgi_request.c.o CMakeFiles/srapath.dir/srapath.c.o -o ../../../bin/srapath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 37%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam-loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam-loader.c.o -MF CMakeFiles/bam-load.dir/bam-loader.c.o.d -o CMakeFiles/bam-load.dir/bam-loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srapath.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srapath srapath.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3.0.3 srapath.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srapath.3 srapath cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 srapath-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 37%] Built target srapath make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader/CMakeFiles/samview.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/bam-loader/CMakeFiles/samview.dir/build.make tools/loaders/bam-loader/CMakeFiles/samview.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 37%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/bam.c.o -MF CMakeFiles/samview.dir/bam.c.o.d -o CMakeFiles/samview.dir/bam.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c [ 37%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/cg_tools.c.o -MF CMakeFiles/sam-dump.dir/cg_tools.c.o.d -o CMakeFiles/sam-dump.dir/cg_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c: In function 'rc_t Usage(const Args*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:579:18: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 579 | for(i = 0; i < argsQty; i++ ) { | ~~^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:585:18: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 585 | for(i = 0; i < argsQty; i++ ) { | ~~^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c: In function 'rc_t KMain(int, char**)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:1304:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1304 | argv[1] = "--help"; | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam-loader.c:1309:19: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 1309 | argv[1] = "--version"; | ^~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'fmt_cigar_elem': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:491:10: warning: unused variable 'rc' [-Wunused-variable] 491 | rc_t rc = string_printf ( dst, 11, &num_writ, "%d%c", cig_oplen, cig_op ); | ^~ [ 37%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump.c.o -MF CMakeFiles/sam-dump.dir/sam-dump.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c [ 37%] Linking C executable ../../../bin/kdbmeta cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/kdbmeta && /usr/bin/cmake -E cmake_link_script CMakeFiles/kdbmeta.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/kdbmeta.dir/kdbmeta.c.o -o ../../../bin/kdbmeta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 38%] Linking C executable ../../../bin/align-info cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/align-info && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-info.dir/link.txt --verbose=1 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'DumpQuality': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:1096:37: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] 1096 | char const newValue = ((param->qualQuant && param->qualQuantSingle)?param->qualQuantSingle:30) + 33; | ^~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here 205 | uint8_t qualQuant[256]; | ^~~~~~~~~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-info.dir/align-info.c.o" -o ../../../bin/align-info /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdbmeta.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kdbmeta kdbmeta.3.0.3 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SetupColumns': cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3.0.3 kdbmeta.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdbmeta.3 kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:3230:10: warning: the comparison will always evaluate as 'true' for the address of 'qualQuant' will never be NULL [-Waddress] 3230 | if ( param -> qualQuant && param -> qualQuantSingle ) { /** we don't really need quality ***/ | ^~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:205:13: note: 'qualQuant' declared here 205 | uint8_t qualQuant[256]; | ^~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Linking CXX executable ../../../bin/check-corrupt cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/check-corrupt.dir/link.txt --verbose=1 [ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/sam-dump3.c.o -MF CMakeFiles/sam-dump.dir/sam-dump3.c.o.d -o CMakeFiles/sam-dump.dir/sam-dump3.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c: In function 'SAM_Dump_Main': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump.c:4380:22: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4380 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ [ 38%] Built target kdbmeta make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/check-corrupt.dir/check-corrupt.cpp.o" -o ../../../bin/check-corrupt /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-info.3.0.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar.dir/build.make tools/loaders/kar/CMakeFiles/kar.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-info align-info.3.0.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Linking C executable ../../../bin/sra-pileup cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-pileup.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3.0.3 align-info.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-info.3 align-info [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar-path.c.o -MF CMakeFiles/kar.dir/kar-path.c.o.d -o CMakeFiles/kar.dir/kar-path.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-pileup.dir/dyn_string.c.o" "CMakeFiles/sra-pileup.dir/cmdline_cmn.c.o" "CMakeFiles/sra-pileup.dir/out_redir.c.o" "CMakeFiles/sra-pileup.dir/perf_log.c.o" "CMakeFiles/sra-pileup.dir/reref.c.o" "CMakeFiles/sra-pileup.dir/cg_tools.c.o" "CMakeFiles/sra-pileup.dir/report_deletes.c.o" "CMakeFiles/sra-pileup.dir/ref_regions.c.o" "CMakeFiles/sra-pileup.dir/4na_ascii.c.o" "CMakeFiles/sra-pileup.dir/ref_walker_0.c.o" "CMakeFiles/sra-pileup.dir/ref_walker.c.o" "CMakeFiles/sra-pileup.dir/walk_debug.c.o" "CMakeFiles/sra-pileup.dir/pileup_counters.c.o" "CMakeFiles/sra-pileup.dir/pileup_index.c.o" "CMakeFiles/sra-pileup.dir/pileup_indels.c.o" "CMakeFiles/sra-pileup.dir/pileup_varcount.c.o" "CMakeFiles/sra-pileup.dir/pileup_stat.c.o" "CMakeFiles/sra-pileup.dir/pileup_v2.c.o" "CMakeFiles/sra-pileup.dir/sra-pileup.c.o" -o ../../../bin/sra-pileup /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 38%] Built target align-info make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/depend /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:557:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 557 | ReportBuildDate( __DATE__ ); | ^~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar+.dir/build.make tools/loaders/kar/CMakeFiles/kar+.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar-path.c.o -MF CMakeFiles/kar+.dir/kar-path.c.o.d -o CMakeFiles/kar+.dir/kar-path.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-path.c In function 'samdump_main', inlined from 'KMain' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:558:26: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:510:10: warning: 'mode' may be used uninitialized [-Wmaybe-uninitialized] 510 | rc = init_out_redir( &redir, mode, opts->outputfile, opts->output_buffer_size ); /* from out_redir.c */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c: In function 'KMain': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/sam-dump3.c:502:25: note: 'mode' was declared here 502 | enum out_redir_mode mode; | ^~~~ [ 38%] Linking C executable ../../../bin/cache-mgr cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-pileup.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/cache-mgr && /usr/bin/cmake -E cmake_link_script CMakeFiles/cache-mgr.dir/link.txt --verbose=1 [ 38%] Building C object tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/sra-pileup/CMakeFiles/sam-dump.dir/dyn_string.c.o -MF CMakeFiles/sam-dump.dir/dyn_string.c.o.d -o CMakeFiles/sam-dump.dir/dyn_string.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/dyn_string.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-pileup sra-pileup.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3.0.3 sra-pileup.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-pileup.3 sra-pileup cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sra-pileup-driver /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/cache-mgr.dir/cache-mgr.c.o" -o ../../../bin/cache-mgr /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Built target sra-pileup make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar/CMakeFiles/kar+meta.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/kar/CMakeFiles/kar+meta.dir/build.make tools/loaders/kar/CMakeFiles/kar+meta.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+util.c.o -MF CMakeFiles/kar+meta.dir/kar+util.c.o.d -o CMakeFiles/kar+meta.dir/kar+util.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+args.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+args.c.o -MF CMakeFiles/kar+.dir/kar+args.c.o.d -o CMakeFiles/kar+.dir/kar+args.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+args.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f check-corrupt.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cache-mgr.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv check-corrupt check-corrupt.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cache-mgr cache-mgr.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3.0.3 cache-mgr.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3.0.3 check-corrupt.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cache-mgr.3 cache-mgr cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s check-corrupt.3 check-corrupt make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Built target cache-mgr make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/DependInfo.cmake "--color=" [ 38%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar-args.c.o -MF CMakeFiles/kar.dir/kar-args.c.o.d -o CMakeFiles/kar.dir/kar-args.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar-args.c [ 38%] Built target check-corrupt make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build.make tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/DependInfo.cmake "--color=" [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -MF CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o.d -o CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dump-blob-boundaries.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 38%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/caps.c.o -MF CMakeFiles/sra-sort.dir/caps.c.o.d -o CMakeFiles/sra-sort.dir/caps.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/DependInfo.cmake "--color=" [ 39%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+print.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+print.c.o -MF CMakeFiles/kar+.dir/kar+print.c.o.d -o CMakeFiles/kar+.dir/kar+print.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+print.c make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build.make tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build.make tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 40%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/caps.c.o -MF CMakeFiles/sra-sort-cg.dir/caps.c.o.d -o CMakeFiles/sra-sort-cg.dir/caps.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/caps.c [ 41%] Linking C executable ../../../bin/vdb-validate cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-validate && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-validate.dir/link.txt --verbose=1 [ 41%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/spot-assembler.c.o -MF CMakeFiles/fastqloader.dir/spot-assembler.c.o.d -o CMakeFiles/fastqloader.dir/spot-assembler.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-validate.dir/vdb-validate.c.o" -o ../../../bin/vdb-validate /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mem.c.o -MF CMakeFiles/sra-sort.dir/mem.c.o.d -o CMakeFiles/sra-sort.dir/mem.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mem.c.o -MF CMakeFiles/sra-sort-cg.dir/mem.c.o.d -o CMakeFiles/sra-sort-cg.dir/mem.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c [ 41%] Building C object tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar.dir/kar.c.o -MF CMakeFiles/kar.dir/kar.c.o.d -o CMakeFiles/kar.dir/kar.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' 33 | FILE_ENTRY ( mem ); | ^~~~~~~~~~ [ 41%] Linking C executable ../../../bin/dump-blob-boundaries cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/dump-blob-boundaries.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/dump-blob-boundaries.dir/dump-blob-boundaries.c.o" -o ../../../bin/dump-blob-boundaries /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mem.c:33:1: note: in expansion of macro 'FILE_ENTRY' 33 | FILE_ENTRY ( mem ); | ^~~~~~~~~~ [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/membank.c.o -MF CMakeFiles/sra-sort.dir/membank.c.o.d -o CMakeFiles/sra-sort.dir/membank.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-validate.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-validate vdb-validate.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3.0.3 vdb-validate.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-validate.3 vdb-validate [ 41%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+util.c.o -MF CMakeFiles/kar+.dir/kar+util.c.o.d -o CMakeFiles/kar+.dir/kar+util.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+util.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/membank.c.o -MF CMakeFiles/sra-sort-cg.dir/membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/membank.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/membank.c [ 41%] Building C object tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o [ 41%] Built target vdb-validate make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+.dir/kar+.c.o -MF CMakeFiles/kar+.dir/kar+.c.o.d -o CMakeFiles/kar+.dir/kar+.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.py.dir/DependInfo.cmake "--color=" [ 41%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f dump-blob-boundaries.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/bam.c.o -MF CMakeFiles/bam-load.dir/bam.c.o.d -o CMakeFiles/bam-load.dir/bam.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv dump-blob-boundaries dump-blob-boundaries.3.0.3 [ 41%] Building C object tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sharq/CMakeFiles/sharq.py.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.py.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/kar\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/kar/CMakeFiles/kar+meta.dir/kar+meta.c.o -MF CMakeFiles/kar+meta.dir/kar+meta.c.o.d -o CMakeFiles/kar+meta.dir/kar+meta.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+meta.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3.0.3 dump-blob-boundaries.3 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E copy /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/sharq.py /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq.py cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s dump-blob-boundaries.3 dump-blob-boundaries make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 41%] Built target dump-blob-boundaries make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/sff-load.dir/DependInfo.cmake "--color=" [ 41%] Built target sharq.py make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/fastq-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build.make tools/loaders/sra-load/CMakeFiles/fastq-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c: In function 'cg_canonical_print_cigar': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1563:25: warning: 'total_cnt' may be used uninitialized [-Wmaybe-uninitialized] 1563 | KOutMsg( "%d%c", total_cnt,op ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1549:16: note: 'total_cnt' was declared here 1549 | int i, total_cnt, cnt; | ^~~~~~~~~ make -f tools/loaders/sra-load/CMakeFiles/sff-load.dir/build.make tools/loaders/sra-load/CMakeFiles/sff-load.dir/build /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1579:12: warning: 'rc' may be used uninitialized [-Wmaybe-uninitialized] 1579 | return rc; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-pileup/cg_tools.c:1547:10: note: 'rc' was declared here 1547 | rc_t rc; | ^~ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/pstring.c.o -MF CMakeFiles/fastq-load.dir/pstring.c.o.d -o CMakeFiles/fastq-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/pstring.c.o -MF CMakeFiles/sff-load.dir/pstring.c.o.d -o CMakeFiles/sff-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-membank.c.o -MF CMakeFiles/sra-sort.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort.dir/paged-membank.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/common-xml.c.o -MF CMakeFiles/fastq-load.dir/common-xml.c.o.d -o CMakeFiles/fastq-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/depend [ 41%] Building C object tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/test-sra\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/test-sra/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/test-sra/CMakeFiles/test-sra.dir/unix/PrintOS.c.o -MF CMakeFiles/test-sra.dir/unix/PrintOS.c.o.d -o CMakeFiles/test-sra.dir/unix/PrintOS.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/test-sra/unix/PrintOS.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:68: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: In lambda function: /usr/include/ncbi-vdb/klib/debug.h:547:27: warning: statement has no effect [-Wunused-value] 547 | #define KDbgSetString(s) ((rc_t)0) | ~^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:464:13: note: in expansion of macro 'KDbgSetString' 464 | KDbgSetString(arg.argument); | ^~~~~~~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/srf-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/srf-load.dir/build.make tools/loaders/sra-load/CMakeFiles/srf-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/pstring.c.o -MF CMakeFiles/srf-load.dir/pstring.c.o.d -o CMakeFiles/srf-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c In function 'kar_persist_karalias', inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:761:14, inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:720:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 720 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:676:28: note: 'total_written' was declared here 676 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ In function 'kar_persist_karfile', inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:748:14, inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:726:9: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:652:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 652 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c: In function 'kar_persist': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar+.c:607:28: note: 'total_written' was declared here 607 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ [ 41%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-membank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-membank.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-membank.c In function 'kar_persist_karalias', inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1067:14, inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1038:9: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1032:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 1032 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c: In function 'kar_persist': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:988:28: note: 'total_written' was declared here 988 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ In function 'kar_persist_karfile', inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1054:14, inlined from 'kar_persist' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:1038:9: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:964:15: warning: 'total_written' may be used uninitialized [-Wmaybe-uninitialized] 964 | *num_writ = total_written; | ~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c: In function 'kar_persist': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/kar/kar.c:919:28: note: 'total_written' was declared here 919 | size_t total_expected, total_written; | ^~~~~~~~~~~~~ [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/experiment-xml.c.o -MF CMakeFiles/fastq-load.dir/experiment-xml.c.o.d -o CMakeFiles/fastq-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3DefaultRowEst': [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/common-xml.c.o -MF CMakeFiles/sff-load.dir/common-xml.c.o.d -o CMakeFiles/sff-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c [ 41%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/run-xml.c.o -MF CMakeFiles/fastq-load.dir/run-xml.c.o.d -o CMakeFiles/fastq-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort.dir/paged-mmapbank.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~ [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -MF CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o.d -o CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/paged-mmapbank.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp: At global scope: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/sratools.cpp:390:13: warning: 'void sratools::do_sratools(const CommandLine&)' defined but not used [-Wunused-function] 390 | static void do_sratools [[noreturn]] (CommandLine const &argv) | ^~~~~~~~~~~ [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/except.c.o -MF CMakeFiles/sra-sort.dir/except.c.o.d -o CMakeFiles/sra-sort.dir/except.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:11540: /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102377:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 102377 | if( pIdx->pPartIdxWhere!=0 ) a[0] -= 10; assert( 10==sqlite3LogEst(2) ); | ^~~~~~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' 42 | FILE_ENTRY ( except ); | ^~~~~~~~~~ make -f tools/loaders/sra-load/CMakeFiles/abi-load.dir/build.make tools/loaders/sra-load/CMakeFiles/abi-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-writer.c.o -MF CMakeFiles/fastqloader.dir/common-writer.c.o.d -o CMakeFiles/fastqloader.dir/common-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/abi-load.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/abi-load.dir/build.make tools/loaders/sra-load/CMakeFiles/abi-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Linking C executable ../../../bin/kar+ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+.dir/link.txt --verbose=1 [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/pstring.c.o -MF CMakeFiles/abi-load.dir/pstring.c.o.d -o CMakeFiles/abi-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/common-xml.c.o -MF CMakeFiles/srf-load.dir/common-xml.c.o.d -o CMakeFiles/srf-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:102378:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 102378 | if( a[0]<33 ) a[0] = 33; assert( 33==sqlite3LogEst(10) ); | ^~~~~~ [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort.dir/idx-mapping.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar+.dir/kar-path.c.o" CMakeFiles/kar+.dir/kar+args.c.o CMakeFiles/kar+.dir/kar+print.c.o CMakeFiles/kar+.dir/kar+util.c.o CMakeFiles/kar+.dir/kar+.c.o -o ../../../bin/kar+ /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/except.c.o -MF CMakeFiles/sra-sort-cg.dir/except.c.o.d -o CMakeFiles/sra-sort-cg.dir/except.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/except.c:42:1: note: in expansion of macro 'FILE_ENTRY' 42 | FILE_ENTRY ( except ); | ^~~~~~~~~~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' 32 | FILE_ENTRY ( idx-mapping ); | ^~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+ kar+.3.0.3 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3.0.3 kar+.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+.3 kar+ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Linking C executable ../../../bin/kar+meta cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar+meta.dir/link.txt --verbose=1 [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -MF CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o.d -o CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c [ 42%] Built target kar+ [ 42%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/common-xml.c.o -MF CMakeFiles/abi-load.dir/common-xml.c.o.d -o CMakeFiles/abi-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/depend /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/kar+meta.dir/kar+util.c.o CMakeFiles/kar+meta.dir/kar+meta.c.o -o ../../../bin/kar+meta /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/illumina-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build.make tools/loaders/sra-load/CMakeFiles/illumina-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 42%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/map-file.c.o -MF CMakeFiles/sra-sort.dir/map-file.c.o.d -o CMakeFiles/sra-sort.dir/map-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c [ 43%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/pstring.c.o -MF CMakeFiles/illumina-load.dir/pstring.c.o.d -o CMakeFiles/illumina-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ctx.h:53:27: warning: '__file__' defined but not used [-Wunused-const-variable=] 53 | static const char __file__ [] = STRINGIZE_DEFINE ( __file_name__ ) | ^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/idx-mapping.c:32:1: note: in expansion of macro 'FILE_ENTRY' 32 | FILE_ENTRY ( idx-mapping ); | ^~~~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar+meta.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar+meta kar+meta.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3.0.3 kar+meta.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar+meta.3 kar+meta make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 43%] Linking C executable ../../../bin/kar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/kar && /usr/bin/cmake -E cmake_link_script CMakeFiles/kar.dir/link.txt --verbose=1 [ 43%] Built target kar+meta make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/helicos-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kar.dir/kar-path.c.o" "CMakeFiles/kar.dir/kar-args.c.o" CMakeFiles/kar.dir/kar.c.o -o ../../../bin/kar /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make -f tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build.make tools/loaders/sra-load/CMakeFiles/helicos-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 44%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-file.c.o -MF CMakeFiles/fastq-load.dir/loader-file.c.o.d -o CMakeFiles/fastq-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 44%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/pstring.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/pstring.c.o -MF CMakeFiles/helicos-load.dir/pstring.c.o.d -o CMakeFiles/helicos-load.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 44%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/map-file.c.o -MF CMakeFiles/sra-sort-cg.dir/map-file.c.o.d -o CMakeFiles/sra-sort-cg.dir/map-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/map-file.c [ 44%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/experiment-xml.c.o -MF CMakeFiles/sff-load.dir/experiment-xml.c.o.d -o CMakeFiles/sff-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 44%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/common-xml.c.o -MF CMakeFiles/helicos-load.dir/common-xml.c.o.d -o CMakeFiles/helicos-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c [ 45%] Linking C executable ../../../bin/vdb-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump.dir/vdb-dump-context.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-coldefs.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-tools.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-str.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-helper.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-formats.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-redir.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump-fastq.c.o" "CMakeFiles/vdb-dump.dir/vdb_info.c.o" "CMakeFiles/vdb-dump.dir/vdb-dump.c.o" -o ../../../bin/vdb-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader-fmt.c.o -MF CMakeFiles/fastq-load.dir/loader-fmt.c.o.d -o CMakeFiles/fastq-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kar.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kar kar.3.0.3 [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/common-xml.c.o -MF CMakeFiles/illumina-load.dir/common-xml.c.o.d -o CMakeFiles/illumina-load.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3.0.3 kar.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kar.3 kar [ 45%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/sequence-writer.c.o -MF CMakeFiles/fastqloader.dir/sequence-writer.c.o.d -o CMakeFiles/fastqloader.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-dump.3.0.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-dump vdb-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3.0.3 vdb-dump.3 [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-dump.3 vdb-dump [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/experiment-xml.c.o -MF CMakeFiles/helicos-load.dir/experiment-xml.c.o.d -o CMakeFiles/helicos-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/experiment-xml.c.o -MF CMakeFiles/srf-load.dir/experiment-xml.c.o.d -o CMakeFiles/srf-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 vdb-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 45%] Built target kar make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/DependInfo.cmake "--color=" [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/sra-writer.c.o -MF CMakeFiles/fastq-load.dir/sra-writer.c.o.d -o CMakeFiles/fastq-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 45%] Built target vdb-dump make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build.make tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 45%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5arrayfile.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMake': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1282:16: warning: 'refSeq' may be used uninitialized [-Wmaybe-uninitialized] 1282 | BAMRefSeq *refSeq; | ^~~~~~ [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/loader.c.o -MF CMakeFiles/fastq-load.dir/loader.c.o.d -o CMakeFiles/fastq-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pstring.c.o -MF CMakeFiles/pacbio-loadxml.dir/pstring.c.o.d -o CMakeFiles/pacbio-loadxml.dir/pstring.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pstring.c [ 45%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/col-pair.c.o -MF CMakeFiles/sra-sort.dir/col-pair.c.o.d -o CMakeFiles/sra-sort.dir/col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 45%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/common-reader.c.o -MF CMakeFiles/fastqloader.dir/common-reader.c.o.d -o CMakeFiles/fastqloader.dir/common-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-illumina.c.o -MF CMakeFiles/fastq-load.dir/writer-illumina.c.o.d -o CMakeFiles/fastq-load.dir/writer-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c [ 45%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5dir.c [ 45%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/run-xml.c.o -MF CMakeFiles/helicos-load.dir/run-xml.c.o.d -o CMakeFiles/helicos-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 46%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/col-pair.c [ 46%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/common-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/common-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/common-xml.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMakeAlignment': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1774:14: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1774 | if (!BAM_AlignmentInit(y, rsltsize, datasize, &y->extra[numExtra])) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1694:13: note: by argument 4 of type 'const void * const' to 'BAM_AlignmentInit' declared here 1694 | static bool BAM_AlignmentInit(BAM_Alignment *const self, unsigned const maxsize, | ^~~~~~~~~~~~~~~~~ [ 46%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/experiment-xml.c.o -MF CMakeFiles/illumina-load.dir/experiment-xml.c.o.d -o CMakeFiles/illumina-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 46%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/experiment-xml.c.o -MF CMakeFiles/abi-load.dir/experiment-xml.c.o.d -o CMakeFiles/abi-load.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 46%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/fastq-reader.c.o -MF CMakeFiles/fastqloader.dir/fastq-reader.c.o.d -o CMakeFiles/fastqloader.dir/fastq-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ [ 47%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/sam.c.o -MF CMakeFiles/samview.dir/sam.c.o.d -o CMakeFiles/samview.dir/sam.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c [ 47%] Linking C executable ../../../bin/test-sra cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/test-sra && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra.dir/test-sra.c.o" "CMakeFiles/test-sra.dir/unix/PrintOS.c.o" -o ../../../bin/test-sra ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/row-set.c.o -MF CMakeFiles/sra-sort.dir/row-set.c.o.d -o CMakeFiles/sra-sort.dir/row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c [ 47%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/hdf5/hdf5file.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-sra.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-sra test-sra.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3.0.3 test-sra.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-sra.3 test-sra make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 47%] Built target test-sra make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load/CMakeFiles/cg-load.dir/DependInfo.cmake "--color=" [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c: In function 'BAM_FileMake': cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-454.c.o -MF CMakeFiles/fastq-load.dir/writer-454.c.o.d -o CMakeFiles/fastq-load.dir/writer-454.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/bam.c:1282:16: warning: 'refSeq' may be used uninitialized [-Wmaybe-uninitialized] 1282 | BAMRefSeq *refSeq; | ^~~~~~ [ 47%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort.dir/simple-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c [ 47%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-ion-torrent.c [ 48%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/cg-load/CMakeFiles/cg-load.dir/build.make tools/loaders/cg-load/CMakeFiles/cg-load.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-file.c.o -MF CMakeFiles/helicos-load.dir/loader-file.c.o.d -o CMakeFiles/helicos-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/run-xml.c.o -MF CMakeFiles/srf-load.dir/run-xml.c.o.d -o CMakeFiles/srf-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 49%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/run-xml.c.o -MF CMakeFiles/illumina-load.dir/run-xml.c.o.d -o CMakeFiles/illumina-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 49%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/run-xml.c.o -MF CMakeFiles/sff-load.dir/run-xml.c.o.d -o CMakeFiles/sff-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 49%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/row-set.c [ 50%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-context.c.o -MF CMakeFiles/pacbio-load.dir/pl-context.c.o.d -o CMakeFiles/pacbio-load.dir/pl-context.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-context.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/cg-load.c: In function 'DB_Fini': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/cg-load.c:229:65: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 229 | if( (rc = KLoaderMeta_Write(node, p->argv0, __DATE__, "Complete Genomics", KAppVersion())) != 0 ) { | ^~~~~~~~ [ 50%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort.dir/mapping-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c [ 50%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/simple-row-set.c [ 50%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader-fmt.c.o -MF CMakeFiles/helicos-load.dir/loader-fmt.c.o.d -o CMakeFiles/helicos-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 50%] Building C object tools/loaders/sra-load/CMakeFiles/fastq-load.dir/fastq-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/fastq-load.dir/fastq-fmt.c.o -MF CMakeFiles/fastq-load.dir/fastq-fmt.c.o.d -o CMakeFiles/fastq-load.dir/fastq-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/fastq-fmt.c [ 50%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-tools.c.o -MF CMakeFiles/pacbio-load.dir/pl-tools.c.o.d -o CMakeFiles/pacbio-load.dir/pl-tools.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-tools.c [ 50%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/sra-writer.c.o -MF CMakeFiles/helicos-load.dir/sra-writer.c.o.d -o CMakeFiles/helicos-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 50%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/mapping-row-set.c [ 50%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c [ 51%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o -MF CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o.d -o CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c [ 51%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/loader.c.o -MF CMakeFiles/helicos-load.dir/loader.c.o.d -o CMakeFiles/helicos-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined 750 | #define YY_BUF_SIZE 16777216 | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:204: note: this is the location of the previous definition 204 | #define YY_BUF_SIZE 16384 | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: In function 'yylex': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1115 | if ( ! yyg->yy_state_buf ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1117 | if ( ! yyg->yy_state_buf ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1120 | if ( ! yyg->yy_start ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c: In function 'Experiment_FillSegAgrep': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/experiment-xml.c:711:21: warning: variable 'b' set but not used [-Wunused-but-set-variable] 711 | const char* b = NULL; | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) | ^~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2395:16: warning: 'yy_top_state' defined but not used [-Wunused-function] 2395 | static int yy_top_state (yyscan_t yyscanner) | ^~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] 1837 | static int input (yyscan_t yyscanner) | ^~~~~ [ 51%] Linking C executable ../../../bin/sra-stat cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-stat && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-stat.dir/link.txt --verbose=1 [ 52%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort.dir/sorting-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-stat.dir/assembly-statistics.c.o" "CMakeFiles/sra-stat.dir/sra.c.o" "CMakeFiles/sra-stat.dir/sra-stat.c.o" -o ../../../bin/sra-stat ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-stat.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-stat sra-stat.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3.0.3 sra-stat.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-stat.3 sra-stat make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 52%] Built target sra-stat make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/CMakeFiles/general-loader.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/CMakeFiles/general-loader.dir/build.make tools/loaders/general-loader/CMakeFiles/general-loader.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 52%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/general-loader.cpp.o -MF CMakeFiles/general-loader.dir/general-loader.cpp.o.d -o CMakeFiles/general-loader.dir/general-loader.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/general-loader.cpp [ 52%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/meta-pair.c.o -MF CMakeFiles/sra-sort.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort.dir/meta-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/run-xml.c.o -MF CMakeFiles/abi-load.dir/run-xml.c.o.d -o CMakeFiles/abi-load.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c [ 52%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-file.c.o -MF CMakeFiles/illumina-load.dir/loader-file.c.o.d -o CMakeFiles/illumina-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 53%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/config.cpp.o -MF CMakeFiles/sratools.dir/config.cpp.o.d -o CMakeFiles/sratools.dir/config.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp [ 53%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -MF CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o.d -o CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sorting-row-set.c [ 53%] Building C object tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-file.c.o -MF CMakeFiles/srf-load.dir/loader-file.c.o.d -o CMakeFiles/srf-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/fastqloader.dir/id2name.c.o -MF CMakeFiles/fastqloader.dir/id2name.c.o.d -o CMakeFiles/fastqloader.dir/id2name.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/writer-helicos.c.o -MF CMakeFiles/helicos-load.dir/writer-helicos.c.o.d -o CMakeFiles/helicos-load.dir/writer-helicos.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-helicos.c [ 53%] Linking C executable ../../../bin/sam-dump cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam-dump.dir/link.txt --verbose=1 [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader-fmt.c.o -MF CMakeFiles/srf-load.dir/loader-fmt.c.o.d -o CMakeFiles/srf-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sam-dump.dir/inputfiles.c.o" "CMakeFiles/sam-dump.dir/perf_log.c.o" "CMakeFiles/sam-dump.dir/rna_splice_log.c.o" "CMakeFiles/sam-dump.dir/sam-dump-opts.c.o" "CMakeFiles/sam-dump.dir/out_redir.c.o" "CMakeFiles/sam-dump.dir/sam-hdr.c.o" "CMakeFiles/sam-dump.dir/sam-hdr1.c.o" "CMakeFiles/sam-dump.dir/matecache.c.o" "CMakeFiles/sam-dump.dir/read_fkt.c.o" "CMakeFiles/sam-dump.dir/sam-aligned.c.o" "CMakeFiles/sam-dump.dir/sam-unaligned.c.o" "CMakeFiles/sam-dump.dir/md_flag.c.o" "CMakeFiles/sam-dump.dir/cg_tools.c.o" "CMakeFiles/sam-dump.dir/sam-dump.c.o" "CMakeFiles/sam-dump.dir/sam-dump3.c.o" "CMakeFiles/sam-dump.dir/dyn_string.c.o" -o ../../../bin/sam-dump /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader-fmt.c.o -MF CMakeFiles/illumina-load.dir/loader-fmt.c.o.d -o CMakeFiles/illumina-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/helicos-load.dir/helicos-fmt.c.o -MF CMakeFiles/helicos-load.dir/helicos-fmt.c.o.d -o CMakeFiles/helicos-load.dir/helicos-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/helicos-fmt.c [ 53%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o [ 53%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-zmw.c.o -MF CMakeFiles/pacbio-load.dir/pl-zmw.c.o.d -o CMakeFiles/pacbio-load.dir/pl-zmw.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-zmw.c [ 53%] Building C object tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/samview.dir/samview.c.o -MF CMakeFiles/samview.dir/samview.c.o.d -o CMakeFiles/samview.dir/samview.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/samview.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/meta-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/meta-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/meta-pair.c [ 53%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/dir-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/dir-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c [ 53%] Linking C executable ../../../bin/fastq-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastq-load.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/fastq-load.dir/pstring.c.o" "CMakeFiles/fastq-load.dir/common-xml.c.o" "CMakeFiles/fastq-load.dir/experiment-xml.c.o" "CMakeFiles/fastq-load.dir/run-xml.c.o" "CMakeFiles/fastq-load.dir/loader-file.c.o" "CMakeFiles/fastq-load.dir/loader-fmt.c.o" "CMakeFiles/fastq-load.dir/sra-writer.c.o" "CMakeFiles/fastq-load.dir/loader.c.o" "CMakeFiles/fastq-load.dir/writer-illumina.c.o" "CMakeFiles/fastq-load.dir/writer-454.c.o" "CMakeFiles/fastq-load.dir/writer-ion-torrent.c.o" "CMakeFiles/fastq-load.dir/fastq-fmt.c.o" -o ../../../bin/fastq-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o [ 53%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-file.c.o -MF CMakeFiles/sff-load.dir/loader-file.c.o.d -o CMakeFiles/sff-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/dir-pair.c.o -MF CMakeFiles/sra-sort.dir/dir-pair.c.o.d -o CMakeFiles/sra-sort.dir/dir-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/dir-pair.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sam-dump.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sam-dump sam-dump.3.0.3 [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/sra-writer.c.o -MF CMakeFiles/illumina-load.dir/sra-writer.c.o.d -o CMakeFiles/illumina-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3.0.3 sam-dump.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sam-dump.3 sam-dump [ 53%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o [ 53%] Linking C static library ../../../ilib/libfastqloader.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sam.c.o -MF CMakeFiles/bam-load.dir/sam.c.o.d -o CMakeFiles/bam-load.dir/sam.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sam.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -P CMakeFiles/fastqloader.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sam-dump-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 53%] Built target sam-dump make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastqloader.dir/link.txt --verbose=1 [ 53%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-intervals.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/DependInfo.cmake "--color=" [ 53%] Linking C executable ../../../bin/samview cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview.dir/link.txt --verbose=1 [ 53%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/sra-writer.c.o -MF CMakeFiles/srf-load.dir/sra-writer.c.o.d -o CMakeFiles/srf-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c /usr/bin/ar qc ../../../ilib/libfastqloader.a "CMakeFiles/fastqloader.dir/spot-assembler.c.o" "CMakeFiles/fastqloader.dir/common-writer.c.o" "CMakeFiles/fastqloader.dir/sequence-writer.c.o" "CMakeFiles/fastqloader.dir/common-reader.c.o" "CMakeFiles/fastqloader.dir/fastq-reader.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-grammar.c.o" "CMakeFiles/fastqloader.dir/zz_fastq-lex.c.o" CMakeFiles/fastqloader.dir/id2name.c.o /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/samview.dir/bam.c.o CMakeFiles/samview.dir/sam.c.o CMakeFiles/samview.dir/samview.c.o -o ../../../bin/samview /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lz make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ranlib ../../../ilib/libfastqloader.a [ 53%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -MF CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o.d -o CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 54%] Built target fastqloader make -f tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/DependInfo.cmake "--color=" [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader-fmt.c.o -MF CMakeFiles/sff-load.dir/loader-fmt.c.o.d -o CMakeFiles/sff-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build.make tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/loader.c.o -MF CMakeFiles/illumina-load.dir/loader.c.o.d -o CMakeFiles/illumina-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 55%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:32: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/../database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o -MF CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o.d -o CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-gw-dumper.cpp [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-file.c.o -MF CMakeFiles/abi-load.dir/loader-file.c.o.d -o CMakeFiles/abi-load.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c [ 55%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o -MF CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o.d -o CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-basecalls_cmn.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/test-general-loader.cpp:619:86: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 619 | REQUIRE_EQ ( string ( __DATE__), GetDbMetadataAttr ( "SOFTWARE/loader", "date" ) ); | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -MF CMakeFiles/pacbio-loadxml.dir/run-xml.c.o.d -o CMakeFiles/pacbio-loadxml.dir/run-xml.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/run-xml.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview samview.3.0.3 [ 55%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-sequence.c.o -MF CMakeFiles/pacbio-load.dir/pl-sequence.c.o.d -o CMakeFiles/pacbio-load.dir/pl-sequence.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-sequence.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3.0.3 samview.3 [ 55%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/tbl-pair.c [ 55%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview.3 samview cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sra-writer.c.o -MF CMakeFiles/sff-load.dir/sra-writer.c.o.d -o CMakeFiles/sff-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 55%] Built target samview make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastq-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastq-load fastq-load.3.0.3 [ 55%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/tbl-pair.c.o -MF CMakeFiles/sra-sort.dir/tbl-pair.c.o.d -o CMakeFiles/sra-sort.dir/tbl-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/tbl-pair.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3.0.3 fastq-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastq-load.3 fastq-load [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/db-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/db-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/db-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build.make tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader-fmt.c.o -MF CMakeFiles/abi-load.dir/loader-fmt.c.o.d -o CMakeFiles/abi-load.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 56%] Built target fastq-load make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/depend [ 56%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/makeinputs.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/makeinputs.cpp.o -MF CMakeFiles/makeinputs.dir/makeinputs.cpp.o.d -o CMakeFiles/makeinputs.dir/makeinputs.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/makeinputs.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o [ 56%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/writer-illumina.c.o -MF CMakeFiles/illumina-load.dir/writer-illumina.c.o.d -o CMakeFiles/illumina-load.dir/writer-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -MF CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o.d -o CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/loader.c.o -MF CMakeFiles/srf-load.dir/loader.c.o.d -o CMakeFiles/srf-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/sra-writer.c.o -MF CMakeFiles/abi-load.dir/sra-writer.c.o.d -o CMakeFiles/abi-load.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 56%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-evidence-dnbs.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c [ 56%] Linking C executable ../../../bin/helicos-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/helicos-load.dir/link.txt --verbose=1 [ 56%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-consensus.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-consensus.c.o -MF CMakeFiles/pacbio-load.dir/pl-consensus.c.o.d -o CMakeFiles/pacbio-load.dir/pl-consensus.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-consensus.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/helicos-load.dir/pstring.c.o" "CMakeFiles/helicos-load.dir/common-xml.c.o" "CMakeFiles/helicos-load.dir/experiment-xml.c.o" "CMakeFiles/helicos-load.dir/run-xml.c.o" "CMakeFiles/helicos-load.dir/loader-file.c.o" "CMakeFiles/helicos-load.dir/loader-fmt.c.o" "CMakeFiles/helicos-load.dir/sra-writer.c.o" "CMakeFiles/helicos-load.dir/loader.c.o" "CMakeFiles/helicos-load.dir/writer-helicos.c.o" "CMakeFiles/helicos-load.dir/helicos-fmt.c.o" -o ../../../bin/helicos-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so [ 56%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/protocol-parser.cpp.o -MF CMakeFiles/general-loader.dir/protocol-parser.cpp.o.d -o CMakeFiles/general-loader.dir/protocol-parser.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/protocol-parser.cpp [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o [ 56%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o -MF CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ref-alignid-col.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/poslen-col-pair.c [ 56%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/loader.c.o -MF CMakeFiles/sff-load.dir/loader.c.o.d -o CMakeFiles/sff-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 57%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/loader.c.o -MF CMakeFiles/abi-load.dir/loader.c.o.d -o CMakeFiles/abi-load.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f helicos-load.3.0.3 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv helicos-load helicos-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3.0.3 helicos-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s helicos-load.3 helicos-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 57%] Built target helicos-load [ 57%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-file.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-file.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/config.cpp:101:13: warning: 'bool sratools::forceInstallID()' defined but not used [-Wunused-function] 101 | static bool forceInstallID(void) | ^~~~~~~~~~~~~~ [ 57%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-passes.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-passes.c.o -MF CMakeFiles/pacbio-load.dir/pl-passes.c.o.d -o CMakeFiles/pacbio-load.dir/pl-passes.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-passes.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 57%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -MF CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o.d -o CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 57%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/db-pair.c.o -MF CMakeFiles/sra-sort.dir/db-pair.c.o.d -o CMakeFiles/sra-sort.dir/db-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/db-pair.c [ 58%] Building C object tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/illumina-load.dir/illumina-fmt.c.o -MF CMakeFiles/illumina-load.dir/illumina-fmt.c.o.d -o CMakeFiles/illumina-load.dir/illumina-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/illumina-fmt.c [ 58%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -MF CMakeFiles/sra-sort-cg.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort-cg.dir/buff-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader-fmt.c [ 59%] Linking CXX executable ../../../../test-bin/test-gw-dumper cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-gw-dumper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-gw-dumper.dir/test-gw-dumper.cpp.o" -o ../../../../test-bin/test-gw-dumper ../../../../ilib/libgeneral-writer.a [ 59%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/command-line.cpp.o -MF CMakeFiles/sratools.dir/command-line.cpp.o.d -o CMakeFiles/sratools.dir/command-line.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/command-line.cpp [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/glob-poslen.c.o -MF CMakeFiles/sra-sort.dir/glob-poslen.c.o.d -o CMakeFiles/sra-sort.dir/glob-poslen.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/glob-poslen.c [ 59%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -MF CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o.d -o CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sra-writer.c [ 59%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-metrics.c.o -MF CMakeFiles/pacbio-load.dir/pl-metrics.c.o.d -o CMakeFiles/pacbio-load.dir/pl-metrics.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-metrics.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 59%] Built target test-gw-dumper make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build.make tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 59%] Building CXX object tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/vschema/CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o -MF CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o.d -o CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/checklookup.cpp [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -MF CMakeFiles/sra-sort.dir/poslen-col-pair.c.o.d -o CMakeFiles/sra-sort.dir/poslen-col-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/poslen-col-pair.c [ 59%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp: In function 'void run(const char*, bool, const int32_t*, const int32_t*, const int8_t*, int)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:76:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 76 | delete gw; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/bio-end/makeinputs.cpp:45:20: note: 'gw' was declared here 45 | GeneralWriter *gw; | ^~ [ 60%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-regions.c.o -MF CMakeFiles/pacbio-load.dir/pl-regions.c.o.d -o CMakeFiles/pacbio-load.dir/pl-regions.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-regions.c [ 60%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/run.c.o -MF CMakeFiles/sra-sort-cg.dir/run.c.o.d -o CMakeFiles/sra-sort-cg.dir/run.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c [ 61%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/alignment-writer.c.o -MF CMakeFiles/bam-load.dir/alignment-writer.c.o.d -o CMakeFiles/bam-load.dir/alignment-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/alignment-writer.c [ 61%] Linking CXX executable ../../../../../test-bin/bio-end-makeinputs [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/bio-end-makeinputs.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf.c.o -MF CMakeFiles/srf-load.dir/srf.c.o.d -o CMakeFiles/srf-load.dir/srf.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf.c /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/bio-end-makeinputs.dir/bio-end/makeinputs.cpp.o" -o ../../../../../test-bin/bio-end-makeinputs ../../../../../ilib/libgeneral-writer.a [ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/ref-alignid-col.c.o -MF CMakeFiles/sra-sort.dir/ref-alignid-col.c.o.d -o CMakeFiles/sra-sort.dir/ref-alignid-col.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/ref-alignid-col.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/loader.c.o -MF CMakeFiles/pacbio-loadxml.dir/loader.c.o.d -o CMakeFiles/pacbio-loadxml.dir/loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c [ 61%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/reference-writer.c.o -MF CMakeFiles/bam-load.dir/reference-writer.c.o.d -o CMakeFiles/bam-load.dir/reference-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/reference-writer.c [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-454.c.o -MF CMakeFiles/sff-load.dir/writer-454.c.o.d -o CMakeFiles/sff-load.dir/writer-454.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-454.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 61%] Built target bio-end-makeinputs make -f tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build.make tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-lock /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/DependInfo.cmake "--color=" [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/writer-absolid.c.o -MF CMakeFiles/abi-load.dir/writer-absolid.c.o.d -o CMakeFiles/abi-load.dir/writer-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build.make tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/build [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-fmt.c.o -MF CMakeFiles/srf-load.dir/srf-fmt.c.o.d -o CMakeFiles/srf-load.dir/srf-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-fmt.c [ 61%] Building C object tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-lock\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/vdb-lock/CMakeFiles/vdb-lock.dir/vdb-lock.c.o -MF CMakeFiles/vdb-lock.dir/vdb-lock.c.o.d -o CMakeFiles/vdb-lock.dir/vdb-lock.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-lock/vdb-lock.c [ 61%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-mappings.c.o -MF CMakeFiles/cg-load.dir/factory-mappings.c.o.d -o CMakeFiles/cg-load.dir/factory-mappings.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c: In function 'WriteSoftwareVersionsMeta': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/loader.c:883:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 883 | rc = KLoaderMeta_Write(node, argv0, __DATE__, fe_name, fe_version); | ^~~~~~~~ [ 61%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -MF CMakeFiles/sra-sort-cg.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort-cg.dir/sra-sort.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c [ 61%] Linking C executable ../../../bin/illumina-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/illumina-load.dir/link.txt --verbose=1 [ 61%] Linking C executable ../../../bin/vdb-lock cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-lock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-lock.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/illumina-load.dir/pstring.c.o" "CMakeFiles/illumina-load.dir/common-xml.c.o" "CMakeFiles/illumina-load.dir/experiment-xml.c.o" "CMakeFiles/illumina-load.dir/run-xml.c.o" "CMakeFiles/illumina-load.dir/loader-file.c.o" "CMakeFiles/illumina-load.dir/loader-fmt.c.o" "CMakeFiles/illumina-load.dir/sra-writer.c.o" "CMakeFiles/illumina-load.dir/loader.c.o" "CMakeFiles/illumina-load.dir/writer-illumina.c.o" "CMakeFiles/illumina-load.dir/illumina-fmt.c.o" -o ../../../bin/illumina-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-lock.dir/vdb-lock.c.o" -o ../../../bin/vdb-lock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 61%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-illumina.c.o -MF CMakeFiles/srf-load.dir/writer-illumina.c.o.d -o CMakeFiles/srf-load.dir/writer-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-illumina.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-lock.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-lock vdb-lock.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3.0.3 vdb-lock.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-lock.3 vdb-lock make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 61%] Built target vdb-lock make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-unlock /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build.make tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 62%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-illumina.c.o -MF CMakeFiles/srf-load.dir/ztr-illumina.c.o.d -o CMakeFiles/srf-load.dir/ztr-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-illumina.c [ 62%] Building C object tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-unlock\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/vdb-unlock/CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o -MF CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o.d -o CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/vdb-unlock/vdb-unlock.c [ 63%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/buff-writer.c.o -MF CMakeFiles/sra-sort.dir/buff-writer.c.o.d -o CMakeFiles/sra-sort.dir/buff-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/buff-writer.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f illumina-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv illumina-load illumina-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3.0.3 illumina-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s illumina-load.3 illumina-load /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings15_Read': make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:248:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 248 | if( tmp[0] < 33 || tmp[0] > 126 ) { | ~~~^~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:225:14: note: 'tmp' declared here 225 | char tmp[2]; | ^~~ [ 64%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/CMakeFiles/makeinputs.dir/testsource.cpp.o -MF CMakeFiles/makeinputs.dir/testsource.cpp.o.d -o CMakeFiles/makeinputs.dir/testsource.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp [ 64%] Linking C executable ../../../bin/vdb-unlock [ 64%] Built target illumina-load make -f tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/vdb-unlock && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-unlock.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/DependInfo.cmake "--color=" In file included from /usr/include/c++/13/ios:42, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/general-writer/general-writer.hpp:34, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:30: In static member function 'static std::size_t std::char_traits::length(const char_type*)', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:648:49, inlined from 'void run(const char*, TestCaseType, const std::string*, int)' at /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:77:25: /usr/include/c++/13/bits/char_traits.h:399:32: warning: 'db_schema' may be used uninitialized [-Wmaybe-uninitialized] 399 | return __builtin_strlen(__s); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp: In function 'void run(const char*, TestCaseType, const std::string*, int)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:57:21: note: 'db_schema' was declared here 57 | const char* db_schema; | ^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:101:16: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 101 | delete gw; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/idx-text/makeinputs.cpp:54:20: note: 'gw' was declared here 54 | GeneralWriter *gw; | ^~ /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-unlock.dir/vdb-unlock.c.o" -o ../../../bin/vdb-unlock /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 64%] Building C object tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/rd-filter-redact/CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o -MF CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o.d -o CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/test-read-write-cursor.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-unlock.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-unlock vdb-unlock.3.0.3 [ 64%] Building C object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/sequence-writer.c.o -MF CMakeFiles/bam-load.dir/sequence-writer.c.o.d -o CMakeFiles/bam-load.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3.0.3 vdb-unlock.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-unlock.3 vdb-unlock make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 64%] Built target vdb-unlock make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/DependInfo.cmake "--color=" [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -MF CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o.d -o CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build.make tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/build /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c: In function 'SequenceWhack': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/sequence-writer.c:490:14: warning: unused variable 'rc' [-Wunused-variable] 490 | rc_t rc = VDatabaseOpenTableUpdate(self->db, &tbl, "SEQUENCE"); | ^~ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pl-progress.c.o -MF CMakeFiles/pacbio-load.dir/pl-progress.c.o.d -o CMakeFiles/pacbio-load.dir/pl-progress.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pl-progress.c [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -MF CMakeFiles/sff-load.dir/writer-ion-torrent.c.o.d -o CMakeFiles/sff-load.dir/writer-ion-torrent.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-ion-torrent.c [ 65%] Building C object tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/rd-filter-redact\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/rd-filter-redact/CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -MF CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o.d -o CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -MF CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o.d -o CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/pacbio-fmt.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings22_Read': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:311:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 311 | if( tmp[0] < 33 || tmp[0] > 126 ) { | ~~~^~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:287:14: note: 'tmp' declared here 287 | char tmp[2]; | ^~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c: In function 'enter_date_name_vers': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/rd-filter-redact/read-filter-redact.c:755:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 755 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); | ^~~~~~~~ [ 65%] Building C object tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/pacbio-load.c.o -MF CMakeFiles/pacbio-load.dir/pacbio-load.c.o.d -o CMakeFiles/pacbio-load.dir/pacbio-load.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c [ 65%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c: In function 'CGMappings25_Read': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:382:16: warning: 'tmp' may be used uninitialized [-Wmaybe-uninitialized] 382 | if( tmp[0] < 33 || tmp[0] > 126 ) { | ~~~^~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-mappings.c:358:14: note: 'tmp' declared here 358 | char tmp[2]; | ^~~ [ 65%] Building C object tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/abi-load.dir/absolid-fmt.c.o -MF CMakeFiles/abi-load.dir/absolid-fmt.c.o.d -o CMakeFiles/abi-load.dir/absolid-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/absolid-fmt.c make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat/CMakeFiles/copycat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/copycat/CMakeFiles/copycat.dir/build.make tools/internal/copycat/CMakeFiles/copycat.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 65%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/copycat.c.o -MF CMakeFiles/copycat.dir/copycat.c.o.d -o CMakeFiles/copycat.dir/copycat.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/copycat.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c: In function 'pacbio_meta_entry': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/pacbio-load/pacbio-load.c:219:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 219 | rc = KLoaderMeta_Write( node, toolname, __DATE__, "PacBio HDF5", KAppVersion() ); | ^~~~~~~~ [ 65%] Linking C executable ../../../bin/pacbio-loadxml cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-loadxml.dir/link.txt --verbose=1 [ 65%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o [ 66%] Linking C executable ../../../bin/test-read-write-cursor cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/loader-imp.c.o -MF CMakeFiles/bam-load.dir/loader-imp.c.o.d -o CMakeFiles/bam-load.dir/loader-imp.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-read-write-cursor.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-loadxml.dir/pstring.c.o" "CMakeFiles/pacbio-loadxml.dir/common-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/experiment-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/run-xml.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-file.c.o" "CMakeFiles/pacbio-loadxml.dir/loader-fmt.c.o" "CMakeFiles/pacbio-loadxml.dir/sra-writer.c.o" "CMakeFiles/pacbio-loadxml.dir/loader.c.o" "CMakeFiles/pacbio-loadxml.dir/pacbio-fmt.c.o" -o ../../../bin/pacbio-loadxml ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-read-write-cursor.dir/test-read-write-cursor.c.o" -o ../../../bin/test-read-write-cursor /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 66%] Building C object tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o [ 66%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/sff-load.dir/sff-fmt.c.o -MF CMakeFiles/sff-load.dir/sff-fmt.c.o.d -o CMakeFiles/sff-load.dir/sff-fmt.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/sff-fmt.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/id-mapper-col.c.o -MF CMakeFiles/sra-sort.dir/id-mapper-col.c.o.d -o CMakeFiles/sra-sort.dir/id-mapper-col.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/id-mapper-col.c [ 66%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -MF CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o.d -o CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/capture-first-half-aligned.c [ 67%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-reads.c.o -MF CMakeFiles/cg-load.dir/factory-reads.c.o.d -o CMakeFiles/cg-load.dir/factory-reads.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-reads.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-read-write-cursor.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-read-write-cursor test-read-write-cursor.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3.0.3 test-read-write-cursor.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-read-write-cursor.3 test-read-write-cursor make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 67%] Linking CXX executable ../../../../../test-bin/idx-text-makeinputs cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-makeinputs.dir/link.txt --verbose=1 [ 67%] Built target test-read-write-cursor make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-makeinputs.dir/idx-text/makeinputs.cpp.o" -o ../../../../../test-bin/idx-text-makeinputs ../../../../../ilib/libgeneral-writer.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build.make tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 67%] Linking C executable ../../../bin/pacbio-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-load.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-loadxml.3.0.3 [ 67%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/context.c.o -MF CMakeFiles/vdb-copy.dir/context.c.o.d -o CMakeFiles/vdb-copy.dir/context.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/context.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-loadxml pacbio-loadxml.3.0.3 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-load.dir/hdf5/hdf5arrayfile.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o" "CMakeFiles/pacbio-load.dir/hdf5/hdf5file.c.o" "CMakeFiles/pacbio-load.dir/pl-context.c.o" "CMakeFiles/pacbio-load.dir/pl-tools.c.o" "CMakeFiles/pacbio-load.dir/pl-zmw.c.o" "CMakeFiles/pacbio-load.dir/pl-basecalls_cmn.c.o" "CMakeFiles/pacbio-load.dir/pl-sequence.c.o" "CMakeFiles/pacbio-load.dir/pl-consensus.c.o" "CMakeFiles/pacbio-load.dir/pl-passes.c.o" "CMakeFiles/pacbio-load.dir/pl-metrics.c.o" "CMakeFiles/pacbio-load.dir/pl-regions.c.o" "CMakeFiles/pacbio-load.dir/pl-progress.c.o" "CMakeFiles/pacbio-load.dir/pacbio-load.c.o" -o ../../../bin/pacbio-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libcrypto.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/lib/x86_64-linux-gnu/libsz.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.a -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3.0.3 pacbio-loadxml.3 [ 67%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-loadxml.3 pacbio-loadxml cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/run.c.o -MF CMakeFiles/sra-sort.dir/run.c.o.d -o CMakeFiles/sra-sort.dir/run.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/run.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 67%] Built target pacbio-loadxml make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/DependInfo.cmake "--color=" [ 67%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/sra-sort.c.o -MF CMakeFiles/sra-sort.dir/sra-sort.c.o.d -o CMakeFiles/sra-sort.dir/sra-sort.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/sra-sort.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build.make tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 67%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/namelist_tools.c.o -MF CMakeFiles/vdb-diff.dir/namelist_tools.c.o.d -o CMakeFiles/vdb-diff.dir/namelist_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/namelist_tools.c [ 67%] Linking C executable ../../../bin/abi-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/abi-load.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Linking C executable ../../../bin/read-filter-redact cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/rd-filter-redact && /usr/bin/cmake -E cmake_link_script CMakeFiles/read-filter-redact.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/abi-load.dir/pstring.c.o" "CMakeFiles/abi-load.dir/common-xml.c.o" "CMakeFiles/abi-load.dir/experiment-xml.c.o" "CMakeFiles/abi-load.dir/run-xml.c.o" "CMakeFiles/abi-load.dir/loader-file.c.o" "CMakeFiles/abi-load.dir/loader-fmt.c.o" "CMakeFiles/abi-load.dir/sra-writer.c.o" "CMakeFiles/abi-load.dir/loader.c.o" "CMakeFiles/abi-load.dir/writer-absolid.c.o" "CMakeFiles/abi-load.dir/absolid-fmt.c.o" -o ../../../bin/abi-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so [ 68%] Built target idx-text-makeinputs make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/read-filter-redact.dir/read-filter-redact.c.o" -o ../../../bin/read-filter-redact /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 68%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-illumina.c.o -MF CMakeFiles/srf-load.dir/srf-illumina.c.o.d -o CMakeFiles/srf-load.dir/srf-illumina.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-illumina.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build.make tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfileformat.c.o -MF CMakeFiles/copycat.dir/ccfileformat.c.o.d -o CMakeFiles/copycat.dir/ccfileformat.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfileformat.c [ 68%] Building C object tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/make-read-filter/CMakeFiles/make-read-filter.dir/make-read-filter.c.o -MF CMakeFiles/make-read-filter.dir/make-read-filter.c.o.d -o CMakeFiles/make-read-filter.dir/make-read-filter.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f read-filter-redact.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv read-filter-redact read-filter-redact.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3.0.3 read-filter-redact.3 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:4172:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4172 | rc = KLoaderMeta_Write(node, progName, __DATE__, "BAM", KAppVersion()); | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s read-filter-redact.3 read-filter-redact make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:33: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.h: In function 'rowCount': cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DSEQUENCE_BEFORE_SECONDARY=0 -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -MF CMakeFiles/sra-sort-cg.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort-cg.dir/csra-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.h:124:16: warning: unused variable 'rc' [-Wunused-variable] 124 | rc_t const rc = VCursorIdRange(curs, cid, first, &count); | ^~ [ 68%] Built target read-filter-redact make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/align-cache /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache/CMakeFiles/align-cache.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: In function 'main_1': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:598:9: warning: ignoring return value of 'chdir' declared with attribute 'warn_unused_result' [-Wunused-result] 598 | chdir(wd); | ^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: In function 'temporaryDirectory': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:938:5: warning: ignoring return value of 'mkdtemp' declared with attribute 'warn_unused_result' [-Wunused-result] 938 | mkdtemp(pattern); | ^~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c: At top level: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/make-read-filter/make-read-filter.c:692:13: warning: 'test' defined but not used [-Wunused-function] 692 | static void test(void) | ^~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/align-cache/CMakeFiles/align-cache.dir/build.make tools/internal/align-cache/CMakeFiles/align-cache.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 68%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o -MF CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o.d -o CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/xcheck-ref-align.c [ 68%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/internal/align-cache/CMakeFiles/align-cache.dir/align-cache.cpp.o -MF CMakeFiles/align-cache.dir/align-cache.cpp.o.d -o CMakeFiles/align-cache.dir/align-cache.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/align-cache/align-cache.cpp [ 68%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/helper.c.o -MF CMakeFiles/vdb-copy.dir/helper.c.o.d -o CMakeFiles/vdb-copy.dir/helper.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/helper.c [ 68%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -MF CMakeFiles/cg-load.dir/factory-tag-lfr.c.o.d -o CMakeFiles/cg-load.dir/factory-tag-lfr.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/factory-tag-lfr.c [ 68%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cccat.c.o -MF CMakeFiles/copycat.dir/cccat.c.o.d -o CMakeFiles/copycat.dir/cccat.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cccat.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f abi-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv abi-load abi-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3.0.3 abi-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s abi-load.3 abi-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/coldefs.c.o -MF CMakeFiles/vdb-diff.dir/coldefs.c.o.d -o CMakeFiles/vdb-diff.dir/coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/coldefs.c [ 69%] Built target abi-load make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/ccextract /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract/CMakeFiles/ccextract.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/ccextract/CMakeFiles/ccextract.dir/build.make tools/internal/ccextract/CMakeFiles/ccextract.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Building C object tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ccextract\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/ccextract/CMakeFiles/ccextract.dir/ccextract.c.o -MF CMakeFiles/ccextract.dir/ccextract.c.o.d -o CMakeFiles/ccextract.dir/ccextract.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/ccextract/ccextract.c [ 69%] Linking C executable ../../../bin/sff-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/sff-load.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sff-load.dir/pstring.c.o" "CMakeFiles/sff-load.dir/common-xml.c.o" "CMakeFiles/sff-load.dir/experiment-xml.c.o" "CMakeFiles/sff-load.dir/run-xml.c.o" "CMakeFiles/sff-load.dir/loader-file.c.o" "CMakeFiles/sff-load.dir/loader-fmt.c.o" "CMakeFiles/sff-load.dir/sra-writer.c.o" "CMakeFiles/sff-load.dir/loader.c.o" "CMakeFiles/sff-load.dir/writer-454.c.o" "CMakeFiles/sff-load.dir/writer-ion-torrent.c.o" "CMakeFiles/sff-load.dir/sff-fmt.c.o" -o ../../../bin/sff-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-load pacbio-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3.0.3 pacbio-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-load.3 pacbio-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff-context.c [ 69%] Linking C executable ../../../bin/sra-sort-cg cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort-cg.dir/link.txt --verbose=1 [ 69%] Built target pacbio-load make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/md5cp /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp/CMakeFiles/md5cp.dir/DependInfo.cmake "--color=" [ 69%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort-cg.dir/caps.c.o" "CMakeFiles/sra-sort-cg.dir/mem.c.o" "CMakeFiles/sra-sort-cg.dir/membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-membank.c.o" "CMakeFiles/sra-sort-cg.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort-cg.dir/except.c.o" "CMakeFiles/sra-sort-cg.dir/idx-mapping.c.o" "CMakeFiles/sra-sort-cg.dir/map-file.c.o" "CMakeFiles/sra-sort-cg.dir/col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/row-set.c.o" "CMakeFiles/sra-sort-cg.dir/simple-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort-cg.dir/meta-pair.c.o" "CMakeFiles/sra-sort-cg.dir/dir-pair.c.o" "CMakeFiles/sra-sort-cg.dir/tbl-pair.c.o" "CMakeFiles/sra-sort-cg.dir/db-pair.c.o" "CMakeFiles/sra-sort-cg.dir/glob-poslen.c.o" "CMakeFiles/sra-sort-cg.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort-cg.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort-cg.dir/buff-writer.c.o" "CMakeFiles/sra-sort-cg.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort-cg.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort-cg.dir/run.c.o" "CMakeFiles/sra-sort-cg.dir/sra-sort.c.o" "CMakeFiles/sra-sort-cg.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort-cg.dir/csra-tbl.c.o" "CMakeFiles/sra-sort-cg.dir/csra-pair.c.o" -o ../../../bin/sra-sort-cg /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/writer-absolid.c.o -MF CMakeFiles/srf-load.dir/writer-absolid.c.o.d -o CMakeFiles/srf-load.dir/writer-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/writer-absolid.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/md5cp/CMakeFiles/md5cp.dir/build.make tools/internal/md5cp/CMakeFiles/md5cp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Building C object tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/md5cp/CMakeFiles/md5cp.dir/md5cp.c.o -MF CMakeFiles/md5cp.dir/md5cp.c.o.d -o CMakeFiles/md5cp.dir/md5cp.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/md5cp/md5cp.c [ 69%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-tbl.c.o -MF CMakeFiles/sra-sort.dir/csra-tbl.c.o.d -o CMakeFiles/sra-sort.dir/csra-tbl.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-tbl.c [ 69%] Building C object tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-sort\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-sort/CMakeFiles/sra-sort.dir/csra-pair.c.o -MF CMakeFiles/sra-sort.dir/csra-pair.c.o.d -o CMakeFiles/sra-sort.dir/csra-pair.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-sort/csra-pair.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sff-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sff-load sff-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3.0.3 sff-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sff-load.3 sff-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Built target sff-load [ 69%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree.c.o -MF CMakeFiles/copycat.dir/cctree.c.o.d -o CMakeFiles/copycat.dir/cctree.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp: In constructor 'TestSource::Buffer::Buffer(const std::string&, uint32_t, uint32_t, bool)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp:52:13: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 8 equals destination size [-Wstringop-truncation] 52 | strncpy ( m_header . dad . signature, p_signature . c_str(), sizeof m_header . dad . signature ); | ^ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort-cg.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort-cg sra-sort-cg.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3.0.3 sra-sort-cg.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort-cg.3 sra-sort-cg make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/cmn.c.o -MF CMakeFiles/vdb-diff.dir/cmn.c.o.d -o CMakeFiles/vdb-diff.dir/cmn.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/cmn.c [ 69%] Built target sra-sort-cg make -f tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build.make tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-cmp /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/DependInfo.cmake "--color=" [ 69%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctree-dump.c.o -MF CMakeFiles/copycat.dir/cctree-dump.c.o.d -o CMakeFiles/copycat.dir/cctree-dump.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctree-dump.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build.make tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 69%] Building C object tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-cmp\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/meta-cmp/CMakeFiles/meta-cmp.dir/meta-cmp.c.o -MF CMakeFiles/meta-cmp.dir/meta-cmp.c.o.d -o CMakeFiles/meta-cmp.dir/meta-cmp.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-cmp/meta-cmp.c [ 69%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/run-source.cpp.o -MF CMakeFiles/sratools.dir/run-source.cpp.o.d -o CMakeFiles/sratools.dir/run-source.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp [ 69%] Linking C executable ../../../bin/md5cp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/md5cp && /usr/bin/cmake -E cmake_link_script CMakeFiles/md5cp.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/md5cp.dir/md5cp.c.o -o ../../../bin/md5cp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 69%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/coldefs.c.o -MF CMakeFiles/vdb-copy.dir/coldefs.c.o.d -o CMakeFiles/vdb-copy.dir/coldefs.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/coldefs.c [ 69%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/row_by_row.c.o -MF CMakeFiles/vdb-diff.dir/row_by_row.c.o.d -o CMakeFiles/vdb-diff.dir/row_by_row.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/row_by_row.c [ 70%] Linking CXX executable ../../../../../test-bin/idx-text-checklookup cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test/vschema && /usr/bin/cmake -E cmake_link_script CMakeFiles/idx-text-checklookup.dir/link.txt --verbose=1 [ 70%] Linking C executable ../../../bin/sra-sort cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-sort && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-sort.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/idx-text-checklookup.dir/idx-text/checklookup.cpp.o" -o ../../../../../test-bin/idx-text-checklookup /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/col_by_col.c.o -MF CMakeFiles/vdb-diff.dir/col_by_col.c.o.d -o CMakeFiles/vdb-diff.dir/col_by_col.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/col_by_col.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-sort.dir/caps.c.o" "CMakeFiles/sra-sort.dir/mem.c.o" "CMakeFiles/sra-sort.dir/membank.c.o" "CMakeFiles/sra-sort.dir/paged-membank.c.o" "CMakeFiles/sra-sort.dir/paged-mmapbank.c.o" "CMakeFiles/sra-sort.dir/except.c.o" "CMakeFiles/sra-sort.dir/idx-mapping.c.o" "CMakeFiles/sra-sort.dir/map-file.c.o" "CMakeFiles/sra-sort.dir/col-pair.c.o" "CMakeFiles/sra-sort.dir/row-set.c.o" "CMakeFiles/sra-sort.dir/simple-row-set.c.o" "CMakeFiles/sra-sort.dir/mapping-row-set.c.o" "CMakeFiles/sra-sort.dir/sorting-row-set.c.o" "CMakeFiles/sra-sort.dir/meta-pair.c.o" "CMakeFiles/sra-sort.dir/dir-pair.c.o" "CMakeFiles/sra-sort.dir/tbl-pair.c.o" "CMakeFiles/sra-sort.dir/db-pair.c.o" "CMakeFiles/sra-sort.dir/glob-poslen.c.o" "CMakeFiles/sra-sort.dir/poslen-col-pair.c.o" "CMakeFiles/sra-sort.dir/ref-alignid-col.c.o" "CMakeFiles/sra-sort.dir/buff-writer.c.o" "CMakeFiles/sra-sort.dir/id-mapper-col.c.o" "CMakeFiles/sra-sort.dir/capture-first-half-aligned.c.o" "CMakeFiles/sra-sort.dir/run.c.o" "CMakeFiles/sra-sort.dir/sra-sort.c.o" "CMakeFiles/sra-sort.dir/xcheck-ref-align.c.o" "CMakeFiles/sra-sort.dir/csra-tbl.c.o" "CMakeFiles/sra-sort.dir/csra-pair.c.o" -o ../../../bin/sra-sort /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lbz2 -llzma [ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f md5cp.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_3.c.o -MF CMakeFiles/cg-load.dir/f1_3.c.o.d -o CMakeFiles/cg-load.dir/f1_3.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_3.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv md5cp md5cp.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s md5cp.3.0.3 md5cp.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s md5cp.3 md5cp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Built target md5cp make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy/CMakeFiles/meta-copy.dir/DependInfo.cmake "--color=" [ 70%] Linking C executable ../../../bin/ccextract cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/ccextract && /usr/bin/cmake -E cmake_link_script CMakeFiles/ccextract.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build.make tools/internal/meta-copy/CMakeFiles/meta-copy.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/ccextract.dir/ccextract.c.o -o ../../../bin/ccextract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libxml2.so [ 70%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o [ 70%] Linking C executable ../../../bin/meta-cmp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-cmp && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-cmp.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/cctar.c.o -MF CMakeFiles/copycat.dir/cctar.c.o.d -o CMakeFiles/copycat.dir/cctar.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c [ 70%] Building C object tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/meta-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/meta-copy/CMakeFiles/meta-copy.dir/meta-copy.c.o -MF CMakeFiles/meta-copy.dir/meta-copy.c.o.d -o CMakeFiles/meta-copy.dir/meta-copy.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c [ 70%] Building C object tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-diff\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-diff/CMakeFiles/vdb-diff.dir/vdb-diff.c.o -MF CMakeFiles/vdb-diff.dir/vdb-diff.c.o.d -o CMakeFiles/vdb-diff.dir/vdb-diff.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-diff/vdb-diff.c [ 70%] Linking C executable ../../../bin/make-read-filter cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/make-read-filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/make-read-filter.dir/link.txt --verbose=1 [ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_5.c.o -MF CMakeFiles/cg-load.dir/f1_5.c.o.d -o CMakeFiles/cg-load.dir/f1_5.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_5.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-cmp.dir/meta-cmp.c.o" -o ../../../bin/meta-cmp /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/make-read-filter.dir/make-read-filter.c.o" -o ../../../bin/make-read-filter /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-sort.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-sort sra-sort.3.0.3 [ 70%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: In function 'KMain': cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-absolid.c.o -MF CMakeFiles/srf-load.dir/ztr-absolid.c.o.d -o CMakeFiles/srf-load.dir/ztr-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-absolid.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:330:23: warning: unused variable 'diffs' [-Wunused-variable] 330 | unsigned long int diffs = 0; | ^~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c: At top level: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/meta-copy/meta-copy.c:186:13: warning: 'cleanup_rc' defined but not used [-Wunused-function] 186 | static void cleanup_rc( void ) { | ^~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c: In function 'what_header_type': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:1015:42: warning: the comparison will always evaluate as 'true' for the address of 'fullsize' will never be NULL [-Waddress] 1015 | header->suntar.extcount && | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/cctar.c:598:25: note: 'fullsize' declared here 598 | sun_fullsize fullsize; /* 502 non-conformant */ | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3.0.3 sra-sort.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-sort.3 sra-sort make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 70%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f1_7.c.o -MF CMakeFiles/cg-load.dir/f1_7.c.o.d -o CMakeFiles/cg-load.dir/f1_7.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f1_7.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f make-read-filter.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv make-read-filter make-read-filter.3.0.3 [ 70%] Built target sra-sort cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3.0.3 make-read-filter.3 make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s make-read-filter.3 make-read-filter cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-cmp.3.0.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-cmp meta-cmp.3.0.3 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3.0.3 meta-cmp.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-cmp.3 meta-cmp [ 70%] Built target idx-text-checklookup [ 70%] Built target make-read-filter make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download/CMakeFiles/test-download.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build.make tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/build [ 71%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccsra.c.o -MF CMakeFiles/copycat.dir/ccsra.c.o.d -o CMakeFiles/copycat.dir/ccsra.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccsra.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/test-download/CMakeFiles/test-download.dir/build.make tools/test-tools/test-download/CMakeFiles/test-download.dir/build [ 71%] Built target meta-cmp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/DependInfo.cmake "--color=" [ 72%] Building C object tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/crc32sum/CMakeFiles/crc32sum.dir/crc32sum.c.o -MF CMakeFiles/crc32sum.dir/crc32sum.c.o.d -o CMakeFiles/crc32sum.dir/crc32sum.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/crc32sum/crc32sum.c [ 73%] Building C object tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/test-download/CMakeFiles/test-download.dir/test-download.c.o -MF CMakeFiles/test-download.dir/test-download.c.o.d -o CMakeFiles/test-download.dir/test-download.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/test-download/test-download.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build.make tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ccextract.3.0.3 [ 73%] Linking C executable ../../../bin/meta-copy cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ccextract ccextract.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/meta-copy && /usr/bin/cmake -E cmake_link_script CMakeFiles/meta-copy.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3.0.3 ccextract.3 [ 73%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ccextract.3 ccextract cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_0.c.o -MF CMakeFiles/cg-load.dir/f2_0.c.o.d -o CMakeFiles/cg-load.dir/f2_0.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_0.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/meta-copy.dir/meta-copy.c.o" -o ../../../bin/meta-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 73%] Building C object tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/kdb-index && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/kdb-index/CMakeFiles/kdb-index.dir/kdb-index.c.o -MF CMakeFiles/kdb-index.dir/kdb-index.c.o.d -o CMakeFiles/kdb-index.dir/kdb-index.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/kdb-index/kdb-index.c [ 73%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/get_platform.c.o -MF CMakeFiles/vdb-copy.dir/get_platform.c.o.d -o CMakeFiles/vdb-copy.dir/get_platform.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/get_platform.c [ 73%] Linking C executable ../../../bin/vdb-diff cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-diff && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-diff.dir/link.txt --verbose=1 [ 73%] Built target ccextract make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-diff.dir/namelist_tools.c.o" "CMakeFiles/vdb-diff.dir/coldefs.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff-context.c.o" "CMakeFiles/vdb-diff.dir/cmn.c.o" "CMakeFiles/vdb-diff.dir/row_by_row.c.o" "CMakeFiles/vdb-diff.dir/col_by_col.c.o" "CMakeFiles/vdb-diff.dir/vdb-diff.c.o" -o ../../../bin/vdb-diff /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build.make tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 73%] Linking C executable ../../../bin/crc32sum cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/crc32sum && /usr/bin/cmake -E cmake_link_script CMakeFiles/crc32sum.dir/link.txt --verbose=1 [ 73%] Building C object tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/pacbio-correct/CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -MF CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o.d -o CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/pacbio-correct/pacbio-correct.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f meta-copy.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv meta-copy meta-copy.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3.0.3 meta-copy.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s meta-copy.3 meta-copy [ 73%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/database-loader.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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CMakeFiles/crc32sum.dir/crc32sum.c.o -o ../../../bin/crc32sum /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 73%] Built target meta-copy make -f tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/build.make tools/test-tools/schema-replace/CMakeFiles/schema-replace.dir/depend [ 73%] Building CXX object tools/internal/align-cache/CMakeFiles/align-cache.dir/helper.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/align-cache\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux 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'/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 73%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/ccfile.c.o -MF CMakeFiles/copycat.dir/ccfile.c.o.d -o CMakeFiles/copycat.dir/ccfile.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/ccfile.c [ 73%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/namelist_tools.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/namelist_tools.c.o -MF CMakeFiles/vdb-copy.dir/namelist_tools.c.o.d -o CMakeFiles/vdb-copy.dir/namelist_tools.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/namelist_tools.c [ 73%] Built target vdb-diff make -f tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/build.make tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/depend [ 73%] Built target crc32sum make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/sortreadtest /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/DependInfo.cmake "--color=" make -f tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/build.make tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/database-loader.cpp:699:90: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 699 | rc = KLoaderMeta_WriteWithVersion ( node, m_programName.c_str(), __DATE__, KAppVersion(), m_softwareName.c_str(), m_softwareVersion ); | ^~~~~~~~ make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/kdb-index.dir/kdb-index.c.o" -o ../../../bin/kdb-index /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 74%] Building C object tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/sortreadtest/CMakeFiles/sortreadtest.dir/sortreadtest.c.o -MF CMakeFiles/sortreadtest.dir/sortreadtest.c.o.d -o CMakeFiles/sortreadtest.dir/sortreadtest.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/sortreadtest/sortreadtest.c make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/samview-util /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util/CMakeFiles/samview-util.dir/DependInfo.cmake "--color=" [ 74%] Building C object tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/rowwritetest/CMakeFiles/rowwritetest.dir/rowwritetest.c.o -MF CMakeFiles/rowwritetest.dir/rowwritetest.c.o.d -o CMakeFiles/rowwritetest.dir/rowwritetest.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c [ 74%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/fileformat.c.o -MF CMakeFiles/copycat.dir/kff/fileformat.c.o.d -o CMakeFiles/copycat.dir/kff/fileformat.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/fileformat.c [ 74%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffext.c.o -MF CMakeFiles/copycat.dir/kff/ffext.c.o.d -o CMakeFiles/copycat.dir/kff/ffext.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffext.c [ 74%] Linking C executable ../../../bin/pacbio-correct cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pacbio-correct && /usr/bin/cmake -E cmake_link_script CMakeFiles/pacbio-correct.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build.make tools/test-tools/samview-util/CMakeFiles/samview-util.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/ztr-huffman.c.o -MF CMakeFiles/srf-load.dir/ztr-huffman.c.o.d -o CMakeFiles/srf-load.dir/ztr-huffman.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/ztr-huffman.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pacbio-correct.dir/pacbio-correct.c.o" -o ../../../bin/pacbio-correct /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 74%] Building C object tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp: In constructor 'data_sources::data_sources(const CommandLine&, const Arguments&, bool)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/run-source.cpp:480:16: warning: unused variable 'havePerm' [-Wunused-variable] 480 | auto const havePerm = perm != nullptr; | ^~~~~~~~ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/samview-util/CMakeFiles/samview-util.dir/samview.c.o -MF CMakeFiles/samview-util.dir/samview.c.o.d -o CMakeFiles/samview-util.dir/samview.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/samview-util/samview.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'run': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:287: warning: "STATUS" redefined 287 | #define STATUS(action) (action FORMAT, tablePath, name) | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:11: /usr/include/ncbi-vdb/klib/status.h:139: note: this is the location of the previous definition 139 | #define STATUS( lvl, ... ) \ | cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f kdb-index.3.0.3 [ 74%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv kdb-index kdb-index.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/copy_meta.c.o -MF CMakeFiles/vdb-copy.dir/copy_meta.c.o.d -o CMakeFiles/vdb-copy.dir/copy_meta.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c [ 74%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_4.c.o -MF CMakeFiles/cg-load.dir/f2_4.c.o.d -o CMakeFiles/cg-load.dir/f2_4.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_4.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdb-index.3.0.3 kdb-index.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s kdb-index.3 kdb-index make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Built target kdb-index make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/testld /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld/CMakeFiles/testld.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pacbio-correct.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pacbio-correct pacbio-correct.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3.0.3 pacbio-correct.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pacbio-correct.3 pacbio-correct make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 74%] Building CXX object tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/CMakeFiles/general-loader.dir/main.cpp.o -MF CMakeFiles/general-loader.dir/main.cpp.o.d -o CMakeFiles/general-loader.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/main.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/testld/CMakeFiles/testld.dir/build.make tools/test-tools/testld/CMakeFiles/testld.dir/build [ 74%] Built target pacbio-correct make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c: In function 'enter_date_name_vers': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/copy_meta.c:349:59: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 349 | rc = KMDataNodeWriteAttr ( node, "build", __DATE__ ); | ^~~~~~~~ [ 74%] Linking C executable ../../../bin/samview-util [ 74%] Linking C executable ../../../bin/test-download cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/test-download && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-download.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/samview-util && /usr/bin/cmake -E cmake_link_script CMakeFiles/samview-util.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build.make tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-download.dir/test-download.c.o" -o ../../../bin/test-download /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 74%] Building C object tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/txt2kdb/CMakeFiles/txt2kdb.dir/txt2kdb.c.o -MF CMakeFiles/txt2kdb.dir/txt2kdb.c.o.d -o CMakeFiles/txt2kdb.dir/txt2kdb.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/txt2kdb/txt2kdb.c [ 74%] Building C object tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/test-tools/testld/CMakeFiles/testld.dir/testld.c.o -MF CMakeFiles/testld.dir/testld.c.o.d -o CMakeFiles/testld.dir/testld.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/testld/testld.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/samview-util.dir/samview.c.o" -o ../../../bin/samview-util /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 75%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/f2_5.c.o -MF CMakeFiles/cg-load.dir/f2_5.c.o.d -o CMakeFiles/cg-load.dir/f2_5.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/f2_5.c [ 75%] Linking CXX executable ../../../../test-bin/makeinputs cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/makeinputs.dir/link.txt --verbose=1 [ 75%] Linking C executable ../../../bin/sortreadtest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/sortreadtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortreadtest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/makeinputs.dir/makeinputs.cpp.o CMakeFiles/makeinputs.dir/testsource.cpp.o -o ../../../../test-bin/makeinputs ../../../../ilib/libgeneral-writer.a -lncbi-vdb cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f test-download.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv test-download test-download.3.0.3 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sortreadtest.dir/sortreadtest.c.o -o ../../../bin/sortreadtest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3.0.3 test-download.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s test-download.3 test-download cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f samview-util.3.0.3 [ 75%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv samview-util samview-util.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffkey.c.o -MF CMakeFiles/copycat.dir/kff/ffkey.c.o.d -o CMakeFiles/copycat.dir/kff/ffkey.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffkey.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3.0.3 samview-util.3 [ 75%] Linking C executable ../../../bin/schema-replace cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s samview-util.3 samview-util cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/schema-replace && /usr/bin/cmake -E cmake_link_script CMakeFiles/schema-replace.dir/link.txt --verbose=1 In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/logger-inl.h:12, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/logger.h:446, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/details/registry-inl.h:12, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/details/registry.h:114, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/spdlog.h:13, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:101: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h: In constructor 'spdlog::pattern_formatter::pattern_formatter(std::string, spdlog::pattern_time_type, std::string, custom_flags)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:110:18: warning: 'spdlog::pattern_formatter::custom_handlers_' will be initialized after [-Wreorder] 110 | custom_flags custom_handlers_; | ^~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:106:10: warning: 'bool spdlog::pattern_formatter::need_localtime_' [-Wreorder] 106 | bool need_localtime_; | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:126: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter-inl.h:1017:15: warning: when initialized here [-Wreorder] 1017 | SPDLOG_INLINE pattern_formatter::pattern_formatter( | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h: In constructor 'spdlog::pattern_formatter::pattern_formatter(spdlog::pattern_time_type, std::string)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:108:26: warning: 'spdlog::pattern_formatter::last_log_secs_' will be initialized after [-Wreorder] 108 | std::chrono::seconds last_log_secs_; | ^~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter.h:106:10: warning: 'bool spdlog::pattern_formatter::need_localtime_' [-Wreorder] 106 | bool need_localtime_; | ^~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/./spdlog/pattern_formatter-inl.h:1031:15: warning: when initialized here [-Wreorder] 1031 | SPDLOG_INLINE pattern_formatter::pattern_formatter(pattern_time_type time_type, std::string eol) | ^~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 75%] Building C object tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/copycat\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/copycat/CMakeFiles/copycat.dir/kff/ffmagic.c.o -MF CMakeFiles/copycat.dir/kff/ffmagic.c.o.d -o CMakeFiles/copycat.dir/kff/ffmagic.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/copycat/kff/ffmagic.c /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/schema-replace.dir/schema-replace.c.o" -o ../../../bin/schema-replace /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 75%] Built target test-download [ 75%] Built target samview-util make -f test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build.make test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/depend /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c: In function 'KMain': make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/rowwritetest/rowwritetest.c:383:17: warning: '__builtin_strncpy' specified bound 512 equals destination size [-Wstringop-truncation] 383 | strncpy (tablePath, pc, sizeof (tablePath)); | ^ [ 75%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o [ 75%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file.c.o -MF CMakeFiles/cg-load.dir/file.c.o.d -o CMakeFiles/cg-load.dir/file.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build.make test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/file-version-factory.c.o -MF CMakeFiles/cg-load.dir/file-version-factory.c.o.d -o CMakeFiles/cg-load.dir/file-version-factory.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/file-version-factory.c make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sortreadtest.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sortreadtest sortreadtest.3.0.3 [ 75%] Building Java objects for test-ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3.0.3 sortreadtest.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClearClassFiles.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sortreadtest.3 sortreadtest make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f schema-replace.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/javac -classpath :/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar:/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar -d /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir @/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_sources cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv schema-replace schema-replace.3.0.3 [ 75%] Built target sortreadtest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3.0.3 schema-replace.3 make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/DependInfo.cmake "--color=" [ 75%] Linking C executable ../../../bin/txt2kdb cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s schema-replace.3 schema-replace cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/txt2kdb && /usr/bin/cmake -E cmake_link_script CMakeFiles/txt2kdb.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/build [ 75%] Linking C executable ../../../bin/testld make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/testld && /usr/bin/cmake -E cmake_link_script CMakeFiles/testld.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/testld.dir/testld.c.o -o ../../../bin/testld /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -MF CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o.d -o CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-build-version.cpp /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/txt2kdb.dir/txt2kdb.c.o -o ../../../bin/txt2kdb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 75%] Built target schema-replace [ 75%] Linking C executable ../../../bin/rowwritetest make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/rowwritetest && /usr/bin/cmake -E cmake_link_script CMakeFiles/rowwritetest.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/DependInfo.cmake "--color=" /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/rowwritetest.dir/rowwritetest.c.o -o ../../../bin/rowwritetest /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 75%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/type_matcher.c.o -MF CMakeFiles/vdb-copy.dir/type_matcher.c.o.d -o CMakeFiles/vdb-copy.dir/type_matcher.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/type_matcher.c [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f txt2kdb.3.0.3 [ 75%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -MF CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o.d -o CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-filepath.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv txt2kdb txt2kdb.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/formats.c.o -MF CMakeFiles/cg-load.dir/formats.c.o.d -o CMakeFiles/cg-load.dir/formats.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/formats.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3.0.3 txt2kdb.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s txt2kdb.3 txt2kdb make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f rowwritetest.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv rowwritetest rowwritetest.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3.0.3 rowwritetest.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s rowwritetest.3 rowwritetest make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 75%] Building C object tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/sra-load/CMakeFiles/srf-load.dir/srf-absolid.c.o -MF CMakeFiles/srf-load.dir/srf-absolid.c.o.d -o CMakeFiles/srf-load.dir/srf-absolid.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sra-load/srf-absolid.c [ 75%] Built target txt2kdb make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/depend [ 75%] Built target rowwritetest make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/DependInfo.cmake "--color=" [ 75%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-algn.c.o -MF CMakeFiles/cg-load.dir/writer-algn.c.o.d -o CMakeFiles/cg-load.dir/writer-algn.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-algn.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o -MF CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o.d -o CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-command-line.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f testld.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv testld testld.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3.0.3 testld.3 [ 75%] Linking C executable ../../../bin/copycat cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/copycat && /usr/bin/cmake -E cmake_link_script CMakeFiles/copycat.dir/link.txt --verbose=1 [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s testld.3 testld cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -MF CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o.d -o CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-json-parse.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/copycat.dir/copycat.c.o CMakeFiles/copycat.dir/ccfileformat.c.o CMakeFiles/copycat.dir/cccat.c.o CMakeFiles/copycat.dir/cctree.c.o "CMakeFiles/copycat.dir/cctree-dump.c.o" CMakeFiles/copycat.dir/cctar.c.o CMakeFiles/copycat.dir/ccsra.c.o CMakeFiles/copycat.dir/ccsubchunk.c.o CMakeFiles/copycat.dir/ccfile.c.o CMakeFiles/copycat.dir/kff/fileformat.c.o CMakeFiles/copycat.dir/kff/ffext.c.o CMakeFiles/copycat.dir/kff/ffkey.c.o CMakeFiles/copycat.dir/kff/ffmagic.c.o -o ../../../bin/copycat /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libmagic.so [ 75%] Built target testld make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 75%] Built target makeinputs make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/DependInfo.cmake "--color=" [ 75%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -MF CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o.d -o CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-sdl-response.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 76%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -MF CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o.d -o CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-accession.cpp [ 77%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/redactval.c.o -MF CMakeFiles/vdb-copy.dir/redactval.c.o.d -o CMakeFiles/vdb-copy.dir/redactval.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/redactval.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f copycat.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv copycat copycat.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3.0.3 copycat.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s copycat.3 copycat make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target copycat make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build.make test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/../../../tools/external/driver-tool -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/driver-tool/CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o -MF CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o.d -o CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool/test-uuid.cpp [ 77%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-copy\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/config_values.c.o -MF CMakeFiles/vdb-copy.dir/config_values.c.o.d -o CMakeFiles/vdb-copy.dir/config_values.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/config_values.c [ 77%] Linking C executable ../../../bin/srf-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sra-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/srf-load.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/srf-load.dir/pstring.c.o" "CMakeFiles/srf-load.dir/common-xml.c.o" "CMakeFiles/srf-load.dir/experiment-xml.c.o" "CMakeFiles/srf-load.dir/run-xml.c.o" "CMakeFiles/srf-load.dir/loader-file.c.o" "CMakeFiles/srf-load.dir/loader-fmt.c.o" "CMakeFiles/srf-load.dir/sra-writer.c.o" "CMakeFiles/srf-load.dir/loader.c.o" "CMakeFiles/srf-load.dir/srf.c.o" "CMakeFiles/srf-load.dir/srf-fmt.c.o" "CMakeFiles/srf-load.dir/writer-illumina.c.o" "CMakeFiles/srf-load.dir/ztr-illumina.c.o" "CMakeFiles/srf-load.dir/srf-illumina.c.o" "CMakeFiles/srf-load.dir/writer-absolid.c.o" "CMakeFiles/srf-load.dir/ztr-absolid.c.o" "CMakeFiles/srf-load.dir/ztr-huffman.c.o" "CMakeFiles/srf-load.dir/srf-absolid.c.o" -o ../../../bin/srf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libkxml.a /usr/lib/x86_64-linux-gnu/libxml2.so [ 77%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-dnbs.c [ 77%] Building C object tools/internal/vdb-copy/CMakeFiles/vdb-copy.dir/vdb-copy.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -MF CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o.d -o CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-evidence-intervals.c [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.cpp.o -MF CMakeFiles/sratools.dir/proc.cpp.o.d -o CMakeFiles/sratools.dir/proc.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f srf-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv srf-load srf-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3.0.3 srf-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s srf-load.3 srf-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building C object tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/cg-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/cg-load/CMakeFiles/cg-load.dir/writer-seq.c.o -MF CMakeFiles/cg-load.dir/writer-seq.c.o.d -o CMakeFiles/cg-load.dir/writer-seq.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/cg-load/writer-seq.c [ 77%] Built target srf-load make -f test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build.make test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build.make test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o [ 77%] Building CXX object test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/vdb-config/CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o -MF CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o.d -o CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-config/test-vdb-config-model.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/uuid.cpp.o -MF CMakeFiles/sratools.dir/uuid.cpp.o.d -o CMakeFiles/sratools.dir/uuid.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/uuid.cpp make -f test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build.make test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build.make test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/build [ 77%] Linking CXX executable ../../../bin/align-cache cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/align-cache && /usr/bin/cmake -E cmake_link_script CMakeFiles/align-cache.dir/link.txt --verbose=1 make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/align-cache.dir/align-cache.cpp.o" "CMakeFiles/align-cache.dir/helper.cpp.o" -o ../../../bin/align-cache /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 77%] Building CXX object test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/external/vdb-dump\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/vdb-dump/CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o -MF CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o.d -o CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-dump/makedb.cpp [ 77%] Linking C executable ../../../bin/cg-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/cg-load && /usr/bin/cmake -E cmake_link_script CMakeFiles/cg-load.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/cg-load.dir/cg-load.c.o" "CMakeFiles/cg-load.dir/factory-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/factory-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/factory-mappings.c.o" "CMakeFiles/cg-load.dir/factory-reads.c.o" "CMakeFiles/cg-load.dir/factory-tag-lfr.c.o" "CMakeFiles/cg-load.dir/f1_3.c.o" "CMakeFiles/cg-load.dir/f1_5.c.o" "CMakeFiles/cg-load.dir/f1_7.c.o" "CMakeFiles/cg-load.dir/f2_0.c.o" "CMakeFiles/cg-load.dir/f2_2.c.o" "CMakeFiles/cg-load.dir/f2_4.c.o" "CMakeFiles/cg-load.dir/f2_5.c.o" "CMakeFiles/cg-load.dir/file.c.o" "CMakeFiles/cg-load.dir/file-version-factory.c.o" "CMakeFiles/cg-load.dir/formats.c.o" "CMakeFiles/cg-load.dir/writer-algn.c.o" "CMakeFiles/cg-load.dir/writer-evidence-dnbs.c.o" "CMakeFiles/cg-load.dir/writer-evidence-intervals.c.o" "CMakeFiles/cg-load.dir/writer-seq.c.o" -o ../../../bin/cg-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 77%] Linking C executable ../../../bin/vdb-copy cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-copy.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f cg-load.3.0.3 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-copy.dir/context.c.o" "CMakeFiles/vdb-copy.dir/helper.c.o" "CMakeFiles/vdb-copy.dir/coldefs.c.o" "CMakeFiles/vdb-copy.dir/get_platform.c.o" "CMakeFiles/vdb-copy.dir/namelist_tools.c.o" "CMakeFiles/vdb-copy.dir/copy_meta.c.o" "CMakeFiles/vdb-copy.dir/type_matcher.c.o" "CMakeFiles/vdb-copy.dir/redactval.c.o" "CMakeFiles/vdb-copy.dir/config_values.c.o" "CMakeFiles/vdb-copy.dir/vdb-copy.c.o" -o ../../../bin/vdb-copy /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv cg-load cg-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3.0.3 cg-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s cg-load.3 cg-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f align-cache.3.0.3 [ 77%] Built target cg-load make -f test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build.make test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv align-cache align-cache.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3.0.3 align-cache.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s align-cache.3 align-cache make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build.make test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target align-cache make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/DependInfo.cmake "--color=" [ 77%] Building C object test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT test/loaders/loader/CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -MF CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o.d -o CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/qfiletest.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-copy.3.0.3 [ 77%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-copy vdb-copy.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/loaders/loader/CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o -MF CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o.d -o CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/test-loaderfile.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3.0.3 vdb-copy.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-copy.3 vdb-copy cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-copy && /usr/bin/cmake -E copy /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy/vdb-copy.kfg /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/vdb-copy.kfg make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target vdb-copy make -f test/loaders/loader/CMakeFiles/Test_LOADER.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADER.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader/CMakeFiles/Test_LOADER.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/loader/CMakeFiles/Test_LOADER.dir/build.make test/loaders/loader/CMakeFiles/Test_LOADER.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/loaders/loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/loaders/loader/CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -MF CMakeFiles/Test_LOADER.dir/loadertest.cpp.o.d -o CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp:307:117: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 307 | REQUIRE_RC ( KLoaderMeta_Write ( node, LoaderName.c_str(), __DATE__, FormatterName.c_str(), KAppVersion() ) ); | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp:321:80: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 321 | REQUIRE_EQ ( string ( __DATE__), GetMetadata ( "SOFTWARE/loader", "date" ) ); | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp:350:143: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 350 | REQUIRE_RC ( KLoaderMeta_WriteWithVersion ( node, LoaderName.c_str(), __DATE__, LoaderVersion, FormatterName.c_str(), KAppVersion() ) ); | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader/loadertest.cpp:364:80: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | REQUIRE_EQ ( string ( __DATE__), GetMetadata ( "SOFTWARE/loader", "date" ) ); | ^ [ 77%] Linking C executable ../../../test-bin/Test_KAPP_qfile cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_KAPP_qfile.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_KAPP_qfile.dir/qfiletest.c.o -o ../../../test-bin/Test_KAPP_qfile ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_KAPP_qfile make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-regexpr.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sharq/CMakeFiles/test-regexpr.dir/build.make test/loaders/sharq/CMakeFiles/test-regexpr.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT test/loaders/sharq/CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -MF CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o.d -o CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/accession.cpp.o -MF CMakeFiles/sratools.dir/accession.cpp.o.d -o CMakeFiles/sratools.dir/accession.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/accession.cpp [ 77%] Linking CXX executable ../../../test-bin/vdb-dump-makedb cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-dump && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-dump-makedb.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-dump-makedb.dir/makedb.cpp.o" -o ../../../test-bin/vdb-dump-makedb /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_BuildVersion cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_BuildVersion.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_BuildVersion.dir/test-build-version.cpp.o" -o ../../../test-bin/Test_Drivertool_BuildVersion make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_BuildVersion make -f test/internal/align/CMakeFiles/Test_Align_samextract.dir/build.make test/internal/align/CMakeFiles/Test_Align_samextract.dir/depend make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/internal/align /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/Test_Align_samextract.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align/CMakeFiles/Test_Align_samextract.dir/build.make test/internal/align/CMakeFiles/Test_Align_samextract.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target vdb-dump-makedb make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_Accession cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++ /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_Accession.dir/link.txt --verbose=1 [ 77%] Building CXX object test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/internal/align/CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o -MF CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o.d -o CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/internal/align/test-samextract.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build.make ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"ngs/ncbi/ngs-c++\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -rdynamic -Wall -MD -MT ngs/ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -MF CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o.d -o CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++/NCBI-NGS.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_Accession.dir/test-accession.cpp.o" -o ../../../test-bin/Test_Drivertool_Accession Note: ngs_test_lib_load.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -E touch /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir/java_compiled_test-ngs-java In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs-c++/NCBI-NGS.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 77%] Generating CMakeFiles/test-ngs-java.dir/java_class_filelist cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClassFilelist.cmake [ 77%] Creating Java archive test-ngs-java.jar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/jar -cf /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar @java_class_filelist make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_Accession make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-doc-jar.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/javadoc/ngs-doc && bash -c /usr/bin/jar\ -cf\ /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-doc.jar\ . cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/ngs-java/CMakeFiles/test-ngs-java.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=test-ngs-java.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.29/Modules/UseJava/Symlinks.cmake [ 77%] Linking CXX executable ../../../test-bin/Test_Drivertool_UUID cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_UUID.dir/link.txt --verbose=1 [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/service.cpp.o -MF CMakeFiles/sratools.dir/service.cpp.o.d -o CMakeFiles/sratools.dir/service.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/service.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_UUID.dir/test-uuid.cpp.o" -o ../../../test-bin/Test_Drivertool_UUID [ 77%] Built target test-ngs-java make -f ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build.make ngs/ngs-java/CMakeFiles/ngs-src-jar.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java && bash -c /usr/bin/jar\ -cf\ /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-src.jar\ \ ngs/ErrorMsg.java\ ngs/Statistics.java\ ngs/Fragment.java\ ngs/FragmentIterator.java\ ngs/Read.java\ ngs/ReadIterator.java\ ngs/ReadGroup.java\ ngs/ReadGroupIterator.java\ ngs/Alignment.java\ ngs/AlignmentIterator.java\ ngs/PileupEvent.java\ ngs/PileupEventIterator.java\ ngs/Pileup.java\ ngs/PileupIterator.java\ ngs/Reference.java\ ngs/ReferenceIterator.java\ ngs/ReadCollection.java\ ngs/Package.java\ ngs/itf/Refcount.java\ ngs/itf/StatisticsItf.java\ ngs/itf/FragmentItf.java\ ngs/itf/FragmentIteratorItf.java\ ngs/itf/ReadItf.java\ ngs/itf/ReadIteratorItf.java\ ngs/itf/ReadGroupItf.java\ ngs/itf/ReadGroupIteratorItf.java\ ngs/itf/AlignmentItf.java\ ngs/itf/AlignmentIteratorItf.java\ ngs/itf/PileupEventItf.java\ ngs/itf/PileupEventIteratorItf.java\ ngs/itf/PileupItf.java\ ngs/itf/PileupIteratorItf.java\ ngs/itf/ReferenceItf.java\ ngs/itf/ReferenceIteratorItf.java\ ngs/itf/ReadCollectionItf.java\ gov/nih/nlm/ncbi/ngs/DownloadManager.java\ gov/nih/nlm/ncbi/ngs/FileCreator.java\ gov/nih/nlm/ncbi/ngs/HttpManager.java\ gov/nih/nlm/ncbi/ngs/LibDependencies.java\ gov/nih/nlm/ncbi/ngs/LibManager.java\ gov/nih/nlm/ncbi/ngs/LibPathIterator.java\ gov/nih/nlm/ncbi/ngs/LibVersionChecker.java\ gov/nih/nlm/ncbi/ngs/LMProperties.java\ gov/nih/nlm/ncbi/ngs/Logger.java\ gov/nih/nlm/ncbi/ngs/Manager.java\ gov/nih/nlm/ncbi/ngs/NGS.java\ gov/nih/nlm/ncbi/ngs/Version.java\ gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java\ gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java\ gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java\ gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp: In member function 'void Construction::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp:40:22: warning: parentheses were disambiguated as a function declaration [-Wvexing-parse] 40 | CRegExprMatcher m( string() ); | ^~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-regexpr.cpp:40:22: note: replace parentheses with braces to declare a variable 40 | CRegExprMatcher m( string() ); | ^~~~~~~~~~~~ | - | { - | } make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target Test_Drivertool_UUID make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build.make ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building Java objects for ngs-examples.jar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClearClassFiles.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/javac -classpath :/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar -d /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir @/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_sources make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target ngs-doc-jar make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/CMakeFiles/gw-dumper.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/CMakeFiles/gw-dumper.dir/build.make libs/general-writer/CMakeFiles/gw-dumper.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/general-writer/CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -MF CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o.d -o CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target ngs-src-jar make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test/CMakeFiles/test-general-writer.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/general-writer/test/CMakeFiles/test-general-writer.dir/build.make libs/general-writer/test/CMakeFiles/test-general-writer.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building CXX object libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/general-writer/test/CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -MF CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o.d -o CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp [ 77%] Linking CXX static library ../../../lib/libncbi-ngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -P CMakeFiles/ncbi-ngs-c++.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ncbi/ngs-c++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-c++.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libncbi-ngs-c++.a "CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" /usr/bin/ranlib ../../../lib/libncbi-ngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs-c++.a.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs-c++.a libncbi-ngs-c++.a.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3.0.3 libncbi-ngs-c++.a.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a.3 libncbi-ngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs-c++.a libncbi-ngs-c++-static.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Built target ncbi-ngs-c++ make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/depend [ 77%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/prefetch /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch/CMakeFiles/prefetch.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/json-parse.cpp.o -MF CMakeFiles/sratools.dir/json-parse.cpp.o.d -o CMakeFiles/sratools.dir/json-parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/json-parse.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/prefetch/CMakeFiles/prefetch.dir/build.make tools/external/prefetch/CMakeFiles/prefetch.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 77%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/kfile-no-q.c.o -MF CMakeFiles/prefetch.dir/kfile-no-q.c.o.d -o CMakeFiles/prefetch.dir/kfile-no-q.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/prefetch/kfile-no-q.c [ 77%] Linking CXX executable ../../../bin/general-loader cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/general-loader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/general-loader.dir/general-loader.cpp.o" "CMakeFiles/general-loader.dir/protocol-parser.cpp.o" "CMakeFiles/general-loader.dir/database-loader.cpp.o" "CMakeFiles/general-loader.dir/main.cpp.o" -o ../../../bin/general-loader ../../../ilib/libgeneral-writer.a ../../../ilib/libloader.a -lkapp ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 78%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfMain.c.o -MF CMakeFiles/prefetch.dir/PrfMain.c.o.d -o CMakeFiles/prefetch.dir/PrfMain.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfMain.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f general-loader.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv general-loader general-loader.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3.0.3 general-loader.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s general-loader.3 general-loader make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 78%] Built target general-loader make -f tools/external/vdb-config/CMakeFiles/vdb-config.dir/build.make tools/external/vdb-config/CMakeFiles/vdb-config.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config/CMakeFiles/vdb-config.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: In function 'void gw_dump::check_vers_component(const char*, const char*, long int, long unsigned int, char)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:1198:29: warning: comparison of integer expressions of different signedness: 'long int' and 'long unsigned int' [-Wsign-compare] 1198 | if ( num < 0 || num > max ) | ~~~~^~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/vdb-config/CMakeFiles/vdb-config.dir/build.make tools/external/vdb-config/CMakeFiles/vdb-config.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 78%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/configure.cpp.o -MF CMakeFiles/vdb-config.dir/configure.cpp.o.d -o CMakeFiles/vdb-config.dir/configure.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/configure.cpp [ 78%] Linking CXX executable ../../../test-bin/Test_Drivertool_CommandLine cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_CommandLine.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_CommandLine.dir/test-command-line.cpp.o" -o ../../../test-bin/Test_Drivertool_CommandLine /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: In function 'const char* gw_dump::metadata_node_root_name(metadata_node_root)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:1315:5: warning: control reaches end of non-void function [-Wreturn-type] 1315 | } | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp: At global scope: /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:732:17: warning: 'char gw_dump::hex(uint8_t)' defined but not used [-Wunused-function] 732 | static char hex(uint8_t const x) { | ^~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:441:10: warning: 'void gw_dump::whack_colname(const T&, char*) [with T = gw_column_evt_v1]' defined but not used [-Wunused-function] 441 | void whack_colname < :: gw_column_evt_v1 > ( const :: gw_column_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:418:12: warning: 'char* gw_dump::read_colname(const T&, FILE*) [with T = gw_column_evt_v1]' defined but not used [-Wunused-function] 418 | char * read_colname < :: gw_column_evt_v1 > ( const :: gw_column_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:368:10: warning: 'void gw_dump::whack_2string(const T&, char*) [with T = gw_2string_evt_v1]' defined but not used [-Wunused-function] 368 | void whack_2string < :: gw_2string_evt_v1 > ( const :: gw_2string_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:345:12: warning: 'char* gw_dump::read_2string(const T&, FILE*) [with T = gw_2string_evt_v1]' defined but not used [-Wunused-function] 345 | char * read_2string < :: gw_2string_evt_v1 > ( const :: gw_2string_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:293:10: warning: 'void gw_dump::whack_1string(const T&, char*) [with T = gw_1string_evt_v1]' defined but not used [-Wunused-function] 293 | void whack_1string < :: gw_1string_evt_v1 > ( const :: gw_1string_evt_v1 & eh, char * string_buffer ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:270:12: warning: 'char* gw_dump::read_1string(const T&, FILE*) [with T = gw_status_evt_v1]' defined but not used [-Wunused-function] 270 | char * read_1string < :: gw_status_evt_v1 > ( const :: gw_status_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/gw-dumper.cpp:255:12: warning: 'char* gw_dump::read_1string(const T&, FILE*) [with T = gw_1string_evt_v1]' defined but not used [-Wunused-function] 255 | char * read_1string < :: gw_1string_evt_v1 > ( const :: gw_1string_evt_v1 & eh, FILE * in ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 78%] Built target Test_Drivertool_CommandLine make -f tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/build.make tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/build.make tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 79%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/spot-assembler.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/spot-assembler.c.o -MF CMakeFiles/latf-load.dir/spot-assembler.c.o.d -o CMakeFiles/latf-load.dir/spot-assembler.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/spot-assembler.c [ 79%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/prefetch.c.o -MF CMakeFiles/prefetch.dir/prefetch.c.o.d -o CMakeFiles/prefetch.dir/prefetch.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/prefetch/prefetch.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp: In function 'void ncbi::runTest(int, const char**, const char*, const char*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:271:13: warning: 'gw' may be used uninitialized [-Wmaybe-uninitialized] 271 | delete gw; | ^~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/test/test-general-writer.cpp:217:24: note: 'gw' was declared here 217 | GeneralWriter *gw; | ^~ [ 79%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/SDL-response.cpp.o -MF CMakeFiles/sratools.dir/SDL-response.cpp.o.d -o CMakeFiles/sratools.dir/SDL-response.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/SDL-response.cpp [ 79%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-writer.c.o -MF CMakeFiles/latf-load.dir/common-writer.c.o.d -o CMakeFiles/latf-load.dir/common-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-writer.c [ 79%] Linking CXX executable ../../../test-bin/test-regexpr cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-regexpr.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-regexpr.dir/test-regexpr.cpp.o" -o ../../../test-bin/test-regexpr /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm -lre2 -labsl_string_view [ 80%] Linking CXX executable ../../../test-bin/test-general-writer cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-writer.dir/link.txt --verbose=1 [ 81%] Linking CXX executable ../../../test-bin/Test_LOADER /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-writer.dir/test-general-writer.cpp.o" -o ../../../test-bin/test-general-writer ../../../ilib/libgeneral-writer.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADER.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/Test_LOADER.dir/loadertest.cpp.o -o ../../../test-bin/Test_LOADER ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -E touch /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir/java_compiled_ngs-examples make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 81%] Generating CMakeFiles/ngs-examples.dir/java_class_filelist cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-java/examples && /usr/bin/cmake -DCMAKE_JAVA_CLASS_OUTPUT_PATH=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir -DCMAKE_JAR_CLASSES_PREFIX= -P /usr/share/cmake-3.29/Modules/UseJava/ClassFilelist.cmake [ 81%] Built target test-regexpr make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/depend [ 81%] Built target test-general-writer make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq/CMakeFiles/sharq.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/loaders/sharq/CMakeFiles/sharq.dir/build.make tools/loaders/sharq/CMakeFiles/sharq.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 81%] Linking CXX executable ../../../test-bin/Test_LOADERFILE make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++.dir/build cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_LOADERFILE.dir/link.txt --verbose=1 [ 81%] Creating Java archive ngs-examples.jar cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/jar -cf /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-examples.jar @java_class_filelist make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 81%] Building CXX object tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/../../.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT tools/loaders/sharq/CMakeFiles/sharq.dir/fastq_parse.cpp.o -MF CMakeFiles/sharq.dir/fastq_parse.cpp.o.d -o CMakeFiles/sharq.dir/fastq_parse.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_LOADERFILE.dir/test-loaderfile.cpp.o" -o ../../../test-bin/Test_LOADERFILE ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 82%] Linking CXX static library ../../lib/libngs-c++.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ngs-c++.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libngs-c++.a "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ranlib ../../lib/libngs-c++.a [ 82%] Built target Test_LOADER make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ngs-c++-shared.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 82%] Linking CXX shared library ../../lib/libngs-c++.so cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-c++-shared.dir/link.txt --verbose=1 [ 82%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/sequence-writer.c.o -MF CMakeFiles/latf-load.dir/sequence-writer.c.o.d -o CMakeFiles/latf-load.dir/sequence-writer.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/sequence-writer.c cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libngs-c++.a.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libngs-c++.a libngs-c++.a.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3.0.3 libngs-c++.a.3 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libngs-c++.so.3 -o ../../lib/libngs-c++.so.3.0.3 "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFilcd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a.3 libngs-c++.a es/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libngs-c++.a libngs-c++-static.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target ngs-c++ make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Linking CXX static library ../../lib/libncbi-ngs.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -P CMakeFiles/ncbi-ngs.dir/cmake_clean_target.cmake /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c: In function 'rc_t FixOverhangingAlignment(KDataBuffer*, uint32_t*, uint32_t, uint32_t, uint32_t)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1540:20: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1540 | if (refend > refLen) { | ~~~~~~~^~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1544:26: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 1544 | if (left * 2 > readlen) { | ~~~~~~~~~^~~~~~~~~ [ 83%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/common-reader.c.o -MF CMakeFiles/latf-load.dir/common-reader.c.o.d -o CMakeFiles/latf-load.dir/common-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/common-reader.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c: In function 'rc_t ProcessBAM(const char*, context_t*, VDatabase*, Reference*, Sequence*, Alignment*, bool*, bool*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:1850:60: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1850 | if (ctx->m_isSingleGroup && ctx->m_emptyGroupIndex == -1) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ [ 83%] Built target Test_LOADERFILE cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs.dir/link.txt --verbose=1 make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build.make ngs/ngs-sdk/CMakeFiles/ncbi-ngs-shared.dir/build /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/loader-imp.c:2340:41: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 2340 | if (!isPrimary && AR_MAPQ(data) < G.minMapQual) make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/ar qc ../../lib/libncbi-ngs.a "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" 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"language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" [ 83%] Linking CXX shared library ../../lib/libncbi-ngs.so cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncbi-ngs-shared.dir/link.txt --verbose=1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libngs-c++.so.3.0.3 ../../lib/libngs-c++.so.3 ../../lib/libngs-c++.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libncbi-ngs.so.3 -o ../../lib/libncbi-ngs.so.3.0.3 "dispatch/CMakeFiles/ngs-disp.dir/ReadCollectionItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReferenceSequenceItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PileupEventItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/AlignmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadGroupItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ReadItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/FragmentItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StatisticsItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/PackageItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/StringItf.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/Refcount.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/VTable.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrBlock.cpp.o" "dispatch/CMakeFiles/ngs-disp.dir/ErrorMsg.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_AlignmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_FragmentIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PackageItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupEventIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_PileupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadCollectionItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadGroupIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReadIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceIteratorItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_ReferenceSequenceItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StatisticsItf.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_Refcount.cpp.o" "language/python/CMakeFiles/ngs-bind-python.dir/py_StringItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadCollectionItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReferenceSequenceItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_PileupEventItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_AlignmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadGroupItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadIteratorItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ReadItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_FragmentItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_StatisticsItf.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Package.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_String.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_Refcount.cpp.o" "language/java/CMakeFiles/ngs-bind-java.dir/jni_ErrorMsg.cpp.o" "../ncbi/ngs/CMakeFiles/ngs.dir/NCBI-NGS.c.o" ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReferenceWindow.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/CSRA1_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/EBI_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_DB_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadGroupInfo.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/SRA_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Statistics.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadCollection.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_PileupEvent.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Pileup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReadGroup.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Alignment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Reference.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceSequence.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Read.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Fragment.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Cursor.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Refcount.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_String.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_Id.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ErrBlock.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_FragmentBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlob.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/NGS_ReferenceBlobIterator.c.o ../ncbi/ngs/CMakeFiles/ngs.dir/VByteBlob.c.o "../ncbi/ngs-c++/CMakeFiles/ncbi-ngs-c++.dir/NCBI-NGS.cpp.o" "../ncbi/ngs-py/CMakeFiles/ngs-py.dir/py_Manager.c.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadCollection.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceSequence.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReferenceIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Reference.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Pileup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEventIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/PileupEvent.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/AlignmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Alignment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroupIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadGroup.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/ReadIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Read.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/FragmentIterator.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Fragment.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/Statistics.cpp.o" "language/c++/CMakeFiles/ngs-bind-c++.dir/StringRef.cpp.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_Manager.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_String.c.o" "../ncbi/ngs-jni/CMakeFiles/ngs-jni.dir/jni_ErrorMsg.c.o" /usr/lib/x86_64-linux-gnu/libkapp.a ../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Built target ngs-c++-shared make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build.make tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-java/examples/CMakeFiles/ngs-examples.dir && /usr/bin/cmake -D_JAVA_TARGET_DIR=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib -D_JAVA_TARGET_OUTPUT_NAME=ngs-examples.jar -D_JAVA_TARGET_OUTPUT_LINK= -P /usr/share/cmake-3.29/Modules/UseJava/Symlinks.cmake [ 83%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -MF CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o.d -o CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 83%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-reader.c.o -MF CMakeFiles/latf-load.dir/fastq-reader.c.o.d -o CMakeFiles/latf-load.dir/fastq-reader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-reader.c [ 83%] Built target ngs-examples make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/DependInfo.cmake "--color=" /usr/bin/ranlib ../../lib/libncbi-ngs.a In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build.make test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/tool-args.cpp.o -MF CMakeFiles/sratools.dir/tool-args.cpp.o.d -o CMakeFiles/sratools.dir/tool-args.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/tool-args.cpp [ 84%] Building CXX object test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/ngs-pileup/CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -MF CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o.d -o CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && rm -f libncbi-ngs.a.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && mv libncbi-ngs.a libncbi-ngs.a.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3.0.3 libncbi-ngs.a.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a.3 libncbi-ngs.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib && ln -f -s libncbi-ngs.a libncbi-ngs-static.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Built target ncbi-ngs make -f test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build.make test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/internal/align /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build.make test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs-pileup/test-ngs-pileup.cpp:37: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 84%] Building CXX object test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/internal/align\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/../ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/internal/align/CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -MF CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o.d -o CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk && /usr/bin/cmake -E cmake_symlink_library ../../lib/libncbi-ngs.so.3.0.3 ../../lib/libncbi-ngs.so.3 ../../lib/libncbi-ngs.so [ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-grammar.c make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 84%] Built target ncbi-ngs-shared make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/depend In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/internal/align/pileup_estimator.cpp:52: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] 97 | bool next = i -> nextPileup (); | ^~~~ [ 84%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT ngs/ngs-sdk/examples/CMakeFiles/FragTest.dir/FragTest.cpp.o -MF CMakeFiles/FragTest.dir/FragTest.cpp.o.d -o CMakeFiles/FragTest.dir/FragTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/FragTest.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 84%] Linking CXX executable ../../../test-bin/Test_Align_samextract cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Align_samextract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o" -o ../../../test-bin/Test_Align_samextract -lsam-extract /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 84%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -MF CMakeFiles/latf-load.dir/zz_fastq-lex.c.o.d -o CMakeFiles/latf-load.dir/zz_fastq-lex.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:750: warning: "YY_BUF_SIZE" redefined 750 | #define YY_BUF_SIZE 16777216 | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:204: note: this is the location of the previous definition 204 | #define YY_BUF_SIZE 16384 | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: In function 'yylex': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 1115 | if ( ! yyg->yy_state_buf ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1117 | if ( ! yyg->yy_state_buf ) | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1117:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1120:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1120 | if ( ! yyg->yy_start ) | ^~ /usr/bin/ld: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c: At top level: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2409:24: warning: 'yy_fatal_error' defined but not used [-Wunused-function] 2409 | static void yynoreturn yy_fatal_error (const char* msg , yyscan_t yyscanner) | ^~~~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:2395:16: warning: 'yy_top_state' defined but not used [-Wunused-function] 2395 | static int yy_top_state (yyscan_t yyscanner) | ^~~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/zz_fastq-lex.c:1837:16: warning: 'input' defined but not used [-Wunused-function] 1837 | static int input (yyscan_t yyscanner) | ^~~~~ CMakeFiles/Test_Align_samextract.dir/test-samextract.cpp.o: in function `extract_buf(char const*, unsigned long, SAMExtractor**) [clone .constprop.0]': ./obj-x86_64-linux-gnu/test/internal/align/./test/internal/align/test-samextract.cpp:117:(.text+0x33b): warning: the use of `tempnam' is dangerous, better use `mkstemp' [ 85%] Linking CXX executable ../../../test-bin/Test_Drivertool_JsonParsing cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_JsonParsing.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_JsonParsing.dir/test-json-parse.cpp.o" -o ../../../test-bin/Test_Drivertool_JsonParsing make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target Test_Drivertool_JsonParsing make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 85%] Linking CXX executable ../../../test-bin/FragTest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragTest.dir/link.txt --verbose=1 [ 85%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignTest.dir/AlignTest.cpp.o -MF CMakeFiles/AlignTest.dir/AlignTest.cpp.o.d -o CMakeFiles/AlignTest.dir/AlignTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/FragTest.dir/FragTest.cpp.o -o ../../../test-bin/FragTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 85%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/util.cpp.o -MF CMakeFiles/vdb-config.dir/util.cpp.o.d -o CMakeFiles/vdb-config.dir/util.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/util.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignTest.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 85%] Built target Test_Align_samextract make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 85%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT ngs/ngs-sdk/examples/CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -MF CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o.d -o CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignSliceTest.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 85%] Built target FragTest make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 86%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT ngs/ngs-sdk/examples/CMakeFiles/PileupTest.dir/PileupTest.cpp.o -MF CMakeFiles/PileupTest.dir/PileupTest.cpp.o.d -o CMakeFiles/PileupTest.dir/PileupTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp: In member function 'void NGS_Pileup::TargetReference::Process(std::ostream&)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/external/ngs-pileup/ngs-pileup.cpp:97:22: warning: unused variable 'next' [-Wunused-variable] 97 | bool next = i -> nextPileup (); | ^~~~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/PileupTest.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/AlignSliceTest.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 86%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/id2name.c.o -MF CMakeFiles/latf-load.dir/id2name.c.o.d -o CMakeFiles/latf-load.dir/id2name.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/id2name.c [ 87%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/fastq-loader.c.o -MF CMakeFiles/latf-load.dir/fastq-loader.c.o.d -o CMakeFiles/latf-load.dir/fastq-loader.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/fastq-loader.c [ 87%] Linking CXX executable ../../../test-bin/PileupTest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/PileupTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/PileupTest.dir/PileupTest.cpp.o -o ../../../test-bin/PileupTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 87%] Building CXX object tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ngs-pileup\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ngs-pileup/CMakeFiles/ngs-pileup.dir/main.cpp.o -MF CMakeFiles/ngs-pileup.dir/main.cpp.o.d -o CMakeFiles/ngs-pileup.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ngs-pileup/main.cpp [ 87%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfRetrier.c.o -MF CMakeFiles/prefetch.dir/PrfRetrier.c.o.d -o CMakeFiles/prefetch.dir/PrfRetrier.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfRetrier.c [ 87%] Building C object tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/prefetch\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/prefetch/CMakeFiles/prefetch.dir/PrfOutFile.c.o -MF CMakeFiles/prefetch.dir/PrfOutFile.c.o.d -o CMakeFiles/prefetch.dir/PrfOutFile.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/prefetch/PrfOutFile.c [ 87%] Linking CXX executable ../../../test-bin/AlignSliceTest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignSliceTest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building C object tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/fastq-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/loaders/fastq-loader/CMakeFiles/latf-load.dir/loader-imp.c.o -MF CMakeFiles/latf-load.dir/loader-imp.c.o.d -o CMakeFiles/latf-load.dir/loader-imp.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignSliceTest.dir/AlignSliceTest.cpp.o -o ../../../test-bin/AlignSliceTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 87%] Built target PileupTest make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/DependInfo.cmake "--color=" [ 87%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/build-version.cpp.o -MF CMakeFiles/sratools.dir/build-version.cpp.o.d -o CMakeFiles/sratools.dir/build-version.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/build-version.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT ngs/ngs-sdk/examples/CMakeFiles/RefTest.dir/RefTest.cpp.o -MF CMakeFiles/RefTest.dir/RefTest.cpp.o.d -o CMakeFiles/RefTest.dir/RefTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/RefTest.cpp [ 87%] Linking CXX executable ../../../test-bin/AlignTest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/AlignTest.dir/link.txt --verbose=1 /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c: In function 'WriteLoaderSignature': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/fastq-loader/loader-imp.c:180:48: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 180 | rc = KLoaderMeta_Write(node, progName, __DATE__, "FASTQ", KAppVersion()); | ^~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/AlignTest.dir/AlignTest.cpp.o -o ../../../test-bin/AlignTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/RefTest.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 87%] Linking C executable ../../../bin/latf-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/fastq-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/latf-load.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/latf-load.dir/spot-assembler.c.o" "CMakeFiles/latf-load.dir/common-writer.c.o" "CMakeFiles/latf-load.dir/sequence-writer.c.o" "CMakeFiles/latf-load.dir/common-reader.c.o" "CMakeFiles/latf-load.dir/fastq-reader.c.o" "CMakeFiles/latf-load.dir/zz_fastq-grammar.c.o" "CMakeFiles/latf-load.dir/zz_fastq-lex.c.o" "CMakeFiles/latf-load.dir/id2name.c.o" "CMakeFiles/latf-load.dir/fastq-loader.c.o" "CMakeFiles/latf-load.dir/loader-imp.c.o" -o ../../../bin/latf-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target AlignSliceTest make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build.make ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT ngs/ngs-sdk/examples/CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -MF CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o.d -o CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f latf-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv latf-load latf-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3.0.3 latf-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s latf-load.3 latf-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target latf-load make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs.dir/ngstest.cpp.o -MF CMakeFiles/test-ngs.dir/ngstest.cpp.o.d -o CMakeFiles/test-ngs.dir/ngstest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target AlignTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/examples/DumpReferenceFASTA.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 87%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o -MF CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o.d -o CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sra.cpp [ 87%] Linking CXX executable ../../../test-bin/Test_Drivertool_FilePath cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_FilePath.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_FilePath.dir/test-filepath.cpp.o" -o ../../../test-bin/Test_Drivertool_FilePath /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 87%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/file-path.posix.cpp.o -MF CMakeFiles/sratools.dir/file-path.posix.cpp.o.d -o CMakeFiles/sratools.dir/file-path.posix.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/file-path.posix.cpp [ 87%] Linking C executable ../../../bin/prefetch cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/prefetch && /usr/bin/cmake -E cmake_link_script CMakeFiles/prefetch.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/prefetch.dir/kfile-no-q.c.o" CMakeFiles/prefetch.dir/PrfMain.c.o CMakeFiles/prefetch.dir/prefetch.c.o CMakeFiles/prefetch.dir/PrfRetrier.c.o CMakeFiles/prefetch.dir/PrfOutFile.c.o -o ../../../bin/prefetch ../../../ilib/libascp.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f prefetch.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv prefetch prefetch.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3.0.3 prefetch.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s prefetch.3 prefetch cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 prefetch-driver make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target prefetch make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o -MF CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o.d -o CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp [ 87%] Linking CXX executable ../../../test-bin/RefTest cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/RefTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/RefTest.dir/RefTest.cpp.o -o ../../../test-bin/RefTest ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target Test_Drivertool_FilePath make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -MF CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o.d -o CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target RefTest make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 87%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -MF CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o.d -o CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_readcollection.cpp [ 87%] Linking CXX executable ../../../test-bin/test-ngs cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs.dir/ngstest.cpp.o" -o ../../../test-bin/test-ngs -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 88%] Linking CXX executable ../../../bin/ngs-pileup cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/ngs-pileup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ngs-pileup.dir/ngs-pileup.cpp.o" "CMakeFiles/ngs-pileup.dir/main.cpp.o" -o ../../../bin/ngs-pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 88%] Linking CXX executable ../../../test-bin/DumpReferenceFASTA cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ngs/ngs-sdk/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/DumpReferenceFASTA.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target test-ngs make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/DumpReferenceFASTA.dir/DumpReferenceFASTA.cpp.o -o ../../../test-bin/DumpReferenceFASTA ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -MF CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o.d -o CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target DumpReferenceFASTA make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o -MF CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o.d -o CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp [ 88%] Linking CXX executable ../../bin/gw-dumper cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/general-writer && /usr/bin/cmake -E cmake_link_script CMakeFiles/gw-dumper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/gw-dumper.dir/gw-dumper.cpp.o" -o ../../bin/gw-dumper ../../ilib/libgeneral-writer.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ngs-pileup.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ngs-pileup ngs-pileup.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3.0.3 ngs-pileup.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ngs-pileup.3 ngs-pileup make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp: In function 'rc_t KMain(int, char**)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_sradb.cpp:864:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 864 | putenv("NCBI_VDB_QUALITY=R"); | ^~~~~~~~~~~~~~~~~~~~ [ 88%] Built target ngs-pileup make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o [ 88%] Built target gw-dumper make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o -MF CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o.d -o CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_reference.cpp make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -MF CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o.d -o CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_fragmentblob.cpp [ 88%] Building CXX object tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/driver-tool\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/driver-tool/CMakeFiles/sratools.dir/proc.posix.cpp.o -MF CMakeFiles/sratools.dir/proc.posix.cpp.o.d -o CMakeFiles/sratools.dir/proc.posix.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp: In member function 'void CSRA1_PileupIterator_AccessAfterNext_PileupGetReferenceBase::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp:191:10: warning: unused variable 'base' [-Wunused-variable] 191 | char base = NGS_PileupGetReferenceBase ( m_pileup, ctx ); | ^~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp: In member function 'void CSRA1_PileupIteratorSlice_AccessAfterNext_PileupGetReferenceBase::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_pileup.cpp:386:10: warning: unused variable 'base' [-Wunused-variable] 386 | char base = NGS_PileupGetReferenceBase ( m_pileup, ctx ); | ^~~~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/bxzstr.hpp:19, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parser.hpp:48, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/fastq_parse.cpp:44: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/strict_fstream.hpp:136:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 136 | catch (std::ios_base::failure e) {} | ^ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/bxzstr.hpp:20: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp: In function 'bxz::Compression bxz::detect_type(char*, char*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:33:19: warning: unused variable 'b3' [-Wunused-variable] 33 | unsigned char b3 = *reinterpret_cast< unsigned char * >(in_buff_start + 3); | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:34:19: warning: unused variable 'b4' [-Wunused-variable] 34 | unsigned char b4 = *reinterpret_cast< unsigned char * >(in_buff_start + 4); | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/sharq/bxzstr/compression_types.hpp:35:19: warning: unused variable 'b5' [-Wunused-variable] 35 | unsigned char b5 = *reinterpret_cast< unsigned char * >(in_buff_start + 5); | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceWindow_Slice_Filtered::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:591:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 591 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:669:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 669 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound_StartInWindow::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:696:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 696 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:719:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 719 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp: In member function 'void CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound_StartInWindow::Instance::test_method()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_csra1_refwin.cpp:740:196: note: '#pragma message: filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags.' 740 | #pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." ) | ^ make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -MF CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o.d -o CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_referenceblob.cpp [ 88%] Linking CXX executable ../../../test-bin/test-vdb-config-model cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-vdb-config-model.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-vdb-config-model.dir/test-vdb-config-model.cpp.o" -o ../../../test-bin/test-vdb-config-model /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target test-vdb-config-model make -f libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o -MF CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o.d -o CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngstest_byteblob.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp: In member function 'POSIX::Process::ExitStatus POSIX::Process::wait() const': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:246:28: warning: 'void std::unexpected()' is deprecated [-Wdeprecated-declarations] 246 | std::unexpected(); | ~~~~~~~~~~~~~~~^~ In file included from /usr/include/c++/13/ios:41, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/driver-tool/proc.posix.cpp:42: /usr/include/c++/13/exception:107:8: note: declared here 107 | void unexpected() __attribute__ ((__noreturn__)); | ^~~~~~~~~~ [ 88%] Linking CXX executable ../../../test-bin/Test_Ngs_Pileup cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs-pileup && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Ngs_Pileup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Ngs_Pileup.dir/test-ngs-pileup.cpp.o" -o ../../../test-bin/Test_Ngs_Pileup ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 88%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/mem-bank.cpp.o -MF CMakeFiles/bam-load.dir/mem-bank.cpp.o.d -o CMakeFiles/bam-load.dir/mem-bank.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/mem-bank.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target Test_Ngs_Pileup make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -MF CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o.d -o CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRAtest.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 88%] Linking CXX executable ../../../test-bin/SlowTest_Align_estimator cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/internal/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/SlowTest_Align_estimator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/SlowTest_Align_estimator.dir/pileup_estimator.cpp.o -o ../../../test-bin/SlowTest_Align_estimator ../../../lib/libncbi-ngs-c++.a ../../../lib/libngs-c++.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 88%] Linking CXX executable ../../../test-bin/Test_Drivertool_SDLResponse cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/Test_Drivertool_SDLResponse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/Test_Drivertool_SDLResponse.dir/test-sdl-response.cpp.o" -o ../../../test-bin/Test_Drivertool_SDLResponse make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target SlowTest_Align_estimator make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o -MF CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o.d -o CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target Test_Drivertool_SDLResponse make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o -MF CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o.d -o CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1test.cpp [ 88%] Building C object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config.c.o -MF CMakeFiles/vdb-config.dir/vdb-config.c.o.d -o CMakeFiles/vdb-config.dir/vdb-config.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config.c In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1test.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 88%] Building CXX object tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/bam-loader\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/usr/include/ncbi-vdb/interfaces/ext -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT tools/loaders/bam-loader/CMakeFiles/bam-load.dir/low-match-count.cpp.o -MF CMakeFiles/bam-load.dir/low-match-count.cpp.o.d -o CMakeFiles/bam-load.dir/low-match-count.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/bam-loader/low-match-count.cpp [ 88%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive.cpp.o -MF CMakeFiles/vdb-config.dir/interactive.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive.cpp [ 88%] Linking CXX executable ../../../bin/sratools cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/driver-tool && /usr/bin/cmake -E cmake_link_script CMakeFiles/sratools.dir/link.txt --verbose=1 /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp: In function 'rc_t KMain(int, char**)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/SRADBtest.cpp:530:12: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 530 | putenv("NCBI_VDB_QUALITY=R"); | ^~~~~~~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sratools.dir/sratools.cpp.o CMakeFiles/sratools.dir/config.cpp.o "CMakeFiles/sratools.dir/command-line.cpp.o" "CMakeFiles/sratools.dir/run-source.cpp.o" CMakeFiles/sratools.dir/proc.cpp.o CMakeFiles/sratools.dir/uuid.cpp.o CMakeFiles/sratools.dir/accession.cpp.o CMakeFiles/sratools.dir/service.cpp.o "CMakeFiles/sratools.dir/json-parse.cpp.o" "CMakeFiles/sratools.dir/SDL-response.cpp.o" "CMakeFiles/sratools.dir/tool-args.cpp.o" "CMakeFiles/sratools.dir/build-version.cpp.o" "CMakeFiles/sratools.dir/file-path.posix.cpp.o" CMakeFiles/sratools.dir/proc.posix.cpp.o -o ../../../bin/sratools /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm [ 88%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/interactive2.cpp.o -MF CMakeFiles/vdb-config.dir/interactive2.cpp.o.d -o CMakeFiles/vdb-config.dir/interactive2.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/interactive2.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sratools.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sratools sratools.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3.0.3 sratools.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sratools.3 sratools make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target sratools make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o -MF CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o.d -o CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1PileupTest.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/ngsfixture.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/CSRA1PileupTest.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 88%] Linking CXX executable ../../../test-bin/test-byteblob cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-byteblob.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-byteblob.dir/ngstest_byteblob.cpp.o" -o ../../../test-bin/test-byteblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 88%] Built target test-byteblob make -f libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build.make libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 89%] Building CXX object libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D_LIBRARY -D__fext__=\"cpp\" -D__file__=\"__FILE__\" -D__mod__=\"NGS_TEST\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/usr/include/ncbi-vdb/../libs/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIE -rdynamic -Wall -MD -MT libs/ngs-vdb/test/CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o -MF CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o.d -o CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/test-ngs-vdb.cpp [ 90%] Building CXX object tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/vdb-config\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/vdb-config/CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -MF CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o.d -o CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/vdb-config/vdb-config-model.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/NGS-VDB.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/test-ngs-vdb.cpp:31: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 90%] Linking CXX executable ../../../test-bin/test-fragmentblob cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-fragmentblob.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-fragmentblob.dir/ngstest_fragmentblob.cpp.o" -o ../../../test-bin/test-fragmentblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 90%] Linking CXX executable ../../../test-bin/test-ngs_csra1_pileup cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_pileup.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_pileup.dir/ngstest_csra1_pileup.cpp.o" -o ../../../test-bin/test-ngs_csra1_pileup -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 90%] Built target test-fragmentblob make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/ref-variation.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ref-variation/CMakeFiles/ref-variation.dir/build.make tools/external/ref-variation/CMakeFiles/ref-variation.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/common.cpp.o -MF CMakeFiles/ref-variation.dir/common.cpp.o.d -o CMakeFiles/ref-variation.dir/common.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Built target test-ngs_csra1_pileup make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation/CMakeFiles/var-expand.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/ref-variation/CMakeFiles/var-expand.dir/build.make tools/external/ref-variation/CMakeFiles/var-expand.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 90%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/common.cpp.o -MF CMakeFiles/var-expand.dir/common.cpp.o.d -o CMakeFiles/var-expand.dir/common.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/common.cpp [ 90%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/helper.cpp.o -MF CMakeFiles/ref-variation.dir/helper.cpp.o.d -o CMakeFiles/ref-variation.dir/helper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp [ 90%] Building CXX object tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/ref-variation\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ref-variation/CMakeFiles/ref-variation.dir/ref-variation.cpp.o -MF CMakeFiles/ref-variation.dir/ref-variation.cpp.o.d -o CMakeFiles/ref-variation.dir/ref-variation.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp [ 90%] Linking CXX executable ../../../bin/vdb-config cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-config.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-config.dir/configure.cpp.o" "CMakeFiles/vdb-config.dir/util.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config.c.o" "CMakeFiles/vdb-config.dir/interactive.cpp.o" "CMakeFiles/vdb-config.dir/interactive2.cpp.o" "CMakeFiles/vdb-config.dir/vdb-config-model.cpp.o" -o ../../../bin/vdb-config ../../../ilib/libtui_cpp.a ../../../ilib/libtui.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:42: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/helper.cpp.o -MF CMakeFiles/var-expand.dir/helper.cpp.o.d -o CMakeFiles/var-expand.dir/helper.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/helper.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-config.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-config vdb-config.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3.0.3 vdb-config.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-config.3 vdb-config cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/vdb-config && /usr/bin/cmake -E copy /usr/include/ncbi-vdb/kfg/ncbi/default.kfg /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/ncbi/default.kfg make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target vdb-config make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/CMakeFiles/sra-search.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/CMakeFiles/sra-search.dir/build.make tools/external/sra-search/CMakeFiles/sra-search.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/main.cpp.o -MF CMakeFiles/sra-search.dir/main.cpp.o.d -o CMakeFiles/sra-search.dir/main.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/main.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/main.cpp:38: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp: In instantiation of 'int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, coverage_info*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:853:47: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, coverage_info*) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:893:43: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector*, TLock*, size_t) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:933:51: required from 'void NSRefVariation::find_alignments(const char*, const std::vector*, TLock*, size_t, const CInputRuns*, KApp::CProgressBar*) [with TLock = KProc::CKLock; size_t = long unsigned int]' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:1024:25: required from here /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:570:28: warning: unused variable 'allele_size' [-Wunused-variable] 570 | size_t allele_size = obj.GetAlleleSize(); | ^~~~~~~~~~~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp: In instantiation of 'int NSRefVariation::find_alignment_in_pileup_db(const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, size_t, TLock*, size_t, coverage_info*, size_t) [with TLock = CNoMutex; size_t = long unsigned int]': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:853:47: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const KSearch::CVRefVariation*, size_t, TLock*, size_t, coverage_info*) [with TLock = CNoMutex; size_t = long unsigned int]' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:893:43: required from 'void NSRefVariation::find_alignments_in_single_run(const char*, const char*, const char*, const char*, const std::vector*, TLock*, size_t) [with TLock = CNoMutex; size_t = long unsigned int]' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:933:51: required from 'void NSRefVariation::find_alignments(const char*, const std::vector*, TLock*, size_t, const CInputRuns*, KApp::CProgressBar*) [with TLock = CNoMutex; size_t = long unsigned int]' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:1051:29: required from here /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/ref-variation.cpp:570:28: warning: unused variable 'allele_size' [-Wunused-variable] [ 91%] Linking CXX executable ../../../test-bin/test-ngs_csra1pileup++ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1pileup++.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1pileup++.dir/CSRA1PileupTest.cpp.o" -o ../../../test-bin/test-ngs_csra1pileup++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target test-ngs_csra1pileup++ make -f tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o -MF CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../searchbuffer.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../vdb-search.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/VdbSearchFixture.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search.cpp:29: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build.make tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp [ 91%] Building CXX object tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/var-expand\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/ref-variation/CMakeFiles/var-expand.dir/var-expand.cpp.o -MF CMakeFiles/var-expand.dir/var-expand.cpp.o.d -o CMakeFiles/var-expand.dir/var-expand.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../searchbuffer.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/../vdb-search.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/VdbSearchFixture.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-sra-search-slow.cpp:28: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Building CXX object tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/.. -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/loaders/general-loader/test/CMakeFiles/test-general-loader.dir/testsource.cpp.o -MF CMakeFiles/test-general-loader.dir/testsource.cpp.o.d -o CMakeFiles/test-general-loader.dir/testsource.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/var-expand.cpp:8: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Linking CXX executable ../../../test-bin/test-ngs_csra1_refwin cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_refwin.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_refwin.dir/ngstest_csra1_refwin.cpp.o" -o ../../../test-bin/test-ngs_csra1_refwin -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c: In function 'sqlite3SelectNew': make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target test-ngs_csra1_refwin make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/DependInfo.cmake "--color=" /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115649:10: warning: function may return address of local variable [-Wreturn-local-addr] 115649 | return pNew; | ^~~~ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build.make tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/test-searchblock.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/vdb-sqlite/sqlite3.c:115609:10: note: declared here 115609 | Select standin; | ^~~~~~~ [ 91%] Linking CXX executable ../../../test-bin/test-ngs_sra_c++ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra_c++.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra_c++.dir/SRAtest.cpp.o" -o ../../../test-bin/test-ngs_sra_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target test-ngs_sra_c++ make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build.make tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp: In constructor 'TestSource::Buffer::Buffer(const std::string&, uint32_t, uint32_t, bool)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/testsource.cpp:52:13: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 8 equals destination size [-Wstringop-truncation] 52 | strncpy ( m_header . dad . signature, p_signature . c_str(), sizeof m_header . dad . signature ); | ^ [ 91%] Building CXX object tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/test-tools/pileup-stats/CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -MF CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o.d -o CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/test-tools/pileup-stats/pileup-stats.cpp:29: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 91%] Linking CXX executable ../../../bin/var-expand cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/var-expand.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/var-expand.dir/common.cpp.o" "CMakeFiles/var-expand.dir/helper.cpp.o" "CMakeFiles/var-expand.dir/var-expand.cpp.o" -o ../../../bin/var-expand ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 91%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/searchblock.cpp.o -MF CMakeFiles/sra-search.dir/searchblock.cpp.o.d -o CMakeFiles/sra-search.dir/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f var-expand.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv var-expand var-expand.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3.0.3 var-expand.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s var-expand.3 var-expand make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Built target var-expand make -f test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build.make test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build.make test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 91%] Building CXX object test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"test/ngs/testy-the-bear\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/ngs -I/build/reproducible-path/sra-sdk-3.0.3+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT test/external/ngs/testy-the-bear/CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -MF CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o.d -o CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp [ 91%] Linking CXX executable ../../../../test-bin/test-general-loader cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-general-loader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-general-loader.dir/test-general-loader.cpp.o" "CMakeFiles/test-general-loader.dir/testsource.cpp.o" -o ../../../../test-bin/test-general-loader ../../../../ilib/libgeneral-writer.a -lkapp -lktst ../../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ncbi/NGS.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:1: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/testy-the-bear/testy-the-bear.cpp:3: /usr/include/ncbi-vdb/kfc/ctx.h:68:19: warning: 's_src_loc' defined but not used [-Wunused-variable] 68 | static KSourceLoc s_src_loc = { __mod__, __file__, __fext__ }; | ^~~~~~~~~ [ 91%] Linking CXX executable ../../../test-bin/test-ngs_reference cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_reference.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_reference.dir/ngstest_reference.cpp.o" -o ../../../test-bin/test-ngs_reference -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 92%] Linking CXX executable ../../../../test-bin/testy-the-bear cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/external/ngs/testy-the-bear && /usr/bin/cmake -E cmake_link_script CMakeFiles/testy-the-bear.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/testy-the-bear.dir/testy-the-bear.cpp.o" -o ../../../../test-bin/testy-the-bear /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a ../../../../lib/libncbi-ngs-c++.a ../../../../lib/libncbi-ngs.a ../../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 92%] Built target test-general-loader [ 92%] Linking CXX executable ../../../bin/ref-variation cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/ref-variation && /usr/bin/cmake -E cmake_link_script CMakeFiles/ref-variation.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/ref-variation.dir/common.cpp.o" "CMakeFiles/ref-variation.dir/helper.cpp.o" "CMakeFiles/ref-variation.dir/ref-variation.cpp.o" -o ../../../bin/ref-variation ../../../ilib/libtk-version.a -lkapp ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 92%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 93%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp [ 93%] Built target testy-the-bear make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 93%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 93%] Built target test-ngs_reference [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f ref-variation.3.0.3 In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv ref-variation ref-variation.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3.0.3 ref-variation.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s ref-variation.3 ref-variation make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target ref-variation [ 94%] Linking CXX executable ../../../test-bin/test-referenceblob cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-referenceblob.dir/link.txt --verbose=1 [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -MF CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-referenceblob.dir/ngstest_referenceblob.cpp.o" -o ../../../test-bin/test-referenceblob -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target test-referenceblob [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 94%] Linking CXX executable ../../../bin/pileup-stats cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pileup-stats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/pileup-stats.dir/pileup-stats.cpp.o" -o ../../../bin/pileup-stats ../../../ilib/libgeneral-writer.a ../../../lib/libncbi-ngs.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -MF CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp [ 94%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -MF CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp [ 94%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 94%] Linking CXX executable ../../../test-bin/test-ngs_sradb cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb.dir/link.txt --verbose=1 [ 94%] Linking CXX executable ../../../../test-bin/test-searchblock cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-searchblock.dir/link.txt --verbose=1 In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-searchblock.dir/test-searchblock.cpp.o" "CMakeFiles/test-searchblock.dir/__/searchblock.cpp.o" -o ../../../../test-bin/test-searchblock ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f pileup-stats.3.0.3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb.dir/ngstest_sradb.cpp.o" -o ../../../test-bin/test-ngs_sradb -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv pileup-stats pileup-stats.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3.0.3 pileup-stats.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s pileup-stats.3 pileup-stats make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 94%] Built target pileup-stats [ 94%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -MF CMakeFiles/sra-search.dir/referencematchiterator.cpp.o.d -o CMakeFiles/sra-search.dir/referencematchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 95%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -MF CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchblock.cpp [ 95%] Built target test-searchblock [ 95%] Building CXX object tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/sra-search\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/CMakeFiles/sra-search.dir/vdb-search.cpp.o -MF CMakeFiles/sra-search.dir/vdb-search.cpp.o.d -o CMakeFiles/sra-search.dir/vdb-search.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp [ 95%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/searchbuffer.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.hpp:36, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/vdb-search.cpp:29: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 95%] Built target test-ngs_sradb [ 95%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] 94 | char ch = complement [ *i ]; | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc/ngs-vdb/VdbReadCollection.hpp:32, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/blobmatchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] 574 | catch ( ngs :: ErrorMsg ex ) | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | [ 95%] Building CXX object tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/test/.. -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -rdynamic -Wall -MD -MT tools/external/sra-search/test/CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -MF CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o.d -o CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] 94 | char ch = complement [ *i ]; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] 574 | catch ( ngs :: ErrorMsg ex ) | ^~ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/StringItf.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/inl/StringRef.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/StringRef.hpp:122, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Fragment.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/FragmentIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/Read.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroup.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadGroupIterator.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/ReadCollection.hpp:31, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/fragmentmatchiterator.hpp:30, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.hpp:35, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:27: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/ngs/itf/Refcount.hpp:30: warning: ignoring '#pragma clang diagnostic' [-Wunknown-pragmas] 30 | #pragma clang diagnostic ignored "-Wtautological-undefined-compare" | /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In function 'std::string ReverseComplementDNA(const std::string&)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:94:32: warning: array subscript has type 'char' [-Wchar-subscripts] 94 | char ch = complement [ *i ]; | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp: In member function 'virtual MatchIterator* ReferenceSearch::NextIterator()': /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/sra-search/referencematchiterator.cpp:574:33: warning: catching polymorphic type 'class ngs::ErrorMsg' by value [-Wcatch-value=] 574 | catch ( ngs :: ErrorMsg ex ) | ^~ [ 95%] Linking CXX executable ../../../test-bin/test-ngs_sradb_c++ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sradb_c++.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sradb_c++.dir/SRADBtest.cpp.o" -o ../../../test-bin/test-ngs_sradb_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 96%] Linking CXX executable ../../../test-bin/test-ngs_csra1_readcollection cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_readcollection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_readcollection.dir/ngstest_csra1_readcollection.cpp.o" -o ../../../test-bin/test-ngs_csra1_readcollection -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 96%] Linking CXX executable ../../../bin/sra-search cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search && /usr/bin/cmake -E cmake_link_script CMakeFiles/sra-search.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/sra-search.dir/main.cpp.o" "CMakeFiles/sra-search.dir/searchblock.cpp.o" "CMakeFiles/sra-search.dir/fragmentmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/blobmatchiterator.cpp.o" "CMakeFiles/sra-search.dir/referencematchiterator.cpp.o" "CMakeFiles/sra-search.dir/vdb-search.cpp.o" -o ../../../bin/sra-search ../../../ilib/libngs-vdb.a ../../../lib/libncbi-ngs.a ../../../ilib/libtk-version.a -Wl,-Bstatic -lkapp -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target test-ngs_sradb_c++ make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target test-ngs_csra1_readcollection cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sra-search.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sra-search sra-search.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3.0.3 sra-search.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sra-search.3 sra-search make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 96%] Built target sra-search [ 96%] Linking CXX executable ../../../test-bin/test-ngs-vdb cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs-vdb.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs-vdb.dir/test-ngs-vdb.cpp.o" -o ../../../test-bin/test-ngs-vdb ../../../ilib/libtk-version.a ../../../ilib/libngs-vdb.a -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a [ 96%] Linking CXX executable ../../../../test-bin/test-sra-search-slow cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search-slow.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search-slow.dir/test-sra-search-slow.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search-slow.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search-slow ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a [ 96%] Built target test-ngs-vdb [ 97%] Linking CXX executable ../../../test-bin/test-ngs_sra cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_sra.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_sra.dir/ngstest_sra.cpp.o" -o ../../../test-bin/test-ngs_sra -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-sra-search-slow [ 97%] Linking CXX executable ../../../../test-bin/test-sra-search cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sra-search.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sra-search.dir/test-sra-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/vdb-search.cpp.o" "CMakeFiles/test-sra-search.dir/__/searchblock.cpp.o" "CMakeFiles/test-sra-search.dir/__/blobmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/fragmentmatchiterator.cpp.o" "CMakeFiles/test-sra-search.dir/__/referencematchiterator.cpp.o" -o ../../../../test-bin/test-sra-search ../../../../ilib/libngs-vdb.a ../../../../lib/libncbi-ngs.a -Wl,-Bstatic -lktst -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_sra [ 97%] Built target test-sra-search [ 97%] Linking CXX executable ../../../test-bin/test-ngs_csra1 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1.dir/ngstest_csra1.cpp.o" -o ../../../test-bin/test-ngs_csra1 -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_csra1 [ 97%] Linking CXX executable ../../../test-bin/test-ngs_csra1_c++ cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/ngs-vdb/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-ngs_csra1_c++.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-ngs_csra1_c++.dir/CSRA1test.cpp.o" -o ../../../test-bin/test-ngs_csra1_c++ -Wl,-Bstatic -lktst -lkapp ../../../lib/libncbi-ngs.a -Wl,-Bdynamic /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target test-ngs_csra1_c++ [ 97%] Linking C static library ../../ilib/libvdb-sqlite.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -P CMakeFiles/vdb-sqlite.dir/cmake_clean_target.cmake cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/libs/vdb-sqlite && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-sqlite.dir/link.txt --verbose=1 /usr/bin/ar qc ../../ilib/libvdb-sqlite.a "CMakeFiles/vdb-sqlite.dir/sqlite3.c.o" "CMakeFiles/vdb-sqlite.dir/sqlite3vdb.c.o" /usr/bin/ranlib ../../ilib/libvdb-sqlite.a make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Built target vdb-sqlite make -f tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build.make tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/depend cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql/CMakeFiles/fastconv.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build.make tools/internal/vdb-sql/CMakeFiles/fastconv.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build.make tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 97%] Building C object tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-sql/CMakeFiles/fastconv.dir/fastconv.c.o -MF CMakeFiles/fastconv.dir/fastconv.c.o.d -o CMakeFiles/fastconv.dir/fastconv.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/fastconv.c [ 98%] Building C object tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/internal/vdb-sql\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11 -rdynamic -Wall -MD -MT tools/internal/vdb-sql/CMakeFiles/vdb-sql.dir/vdb_shell.c.o -MF CMakeFiles/vdb-sql.dir/vdb_shell.c.o.d -o CMakeFiles/vdb-sql.dir/vdb_shell.c.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-sql/vdb_shell.c [ 98%] Linking C executable ../../../bin/fastconv cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cmake -E cmake_link_script CMakeFiles/fastconv.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/fastconv.dir/fastconv.c.o -o ../../../bin/fastconv /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a ../../../ilib/libvdb-sqlite.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f fastconv.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv fastconv fastconv.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3.0.3 fastconv.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s fastconv.3 fastconv make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target fastconv [ 98%] Linking C executable ../../../bin/vdb-sql cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/internal/vdb-sql && /usr/bin/cmake -E cmake_link_script CMakeFiles/vdb-sql.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/vdb-sql.dir/vdb_shell.c.o" -o ../../../bin/vdb-sql ../../../ilib/libvdb-sqlite.a ../../../ilib/libngs.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f vdb-sql.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv vdb-sql vdb-sql.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3.0.3 vdb-sql.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s vdb-sql.3 vdb-sql make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target vdb-sql [ 98%] Linking CXX executable ../../../bin/bam-load cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/bam-loader && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam-load.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/bam-load.dir/bam-loader.c.o" "CMakeFiles/bam-load.dir/bam.c.o" "CMakeFiles/bam-load.dir/sam.c.o" "CMakeFiles/bam-load.dir/alignment-writer.c.o" "CMakeFiles/bam-load.dir/reference-writer.c.o" "CMakeFiles/bam-load.dir/sequence-writer.c.o" "CMakeFiles/bam-load.dir/loader-imp.c.o" "CMakeFiles/bam-load.dir/mem-bank.cpp.o" "CMakeFiles/bam-load.dir/low-match-count.cpp.o" -o ../../../bin/bam-load ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm ../../../ilib/libloader.a /usr/lib/x86_64-linux-gnu/libssl.so /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libncbi-wvdb.so -lpthread -ldl -lm -lz /usr/lib/x86_64-linux-gnu/libcrypto.so cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f bam-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv bam-load bam-load.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3.0.3 bam-load.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s bam-load.3 bam-load make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target bam-load [ 99%] Linking CXX executable ../../../bin/sharq cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/sharq.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/sharq.dir/fastq_parse.cpp.o -o ../../../bin/sharq -lstdc++fs /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libbz2.so -lre2 -labsl_string_view cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && rm -f sharq.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && mv sharq sharq.3.0.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sharq.3.0.3 sharq.3 cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin && ln -f -s sharq.3 sharq make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target sharq make -f test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/depend make -f test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/depend make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sra-sdk-3.0.3+dfsg /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make -f test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build.make test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/build make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Building CXX object test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/../../../tools/loaders/sharq -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT test/loaders/sharq/CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o -MF CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o.d -o CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-sharq-writer.cpp [ 99%] Building CXX object test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/c++ -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/inc -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/ilib/include -I/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/../../../tools/loaders/sharq -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -rdynamic -Wall -MD -MT test/loaders/sharq/CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o -MF CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o.d -o CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o -c /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-sharq-parser.cpp In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/bxzstr.hpp:19, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/fastq_parser.hpp:48, from /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/test-sharq-parser.cpp:37: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/strict_fstream.hpp:136:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 136 | catch (std::ios_base::failure e) {} | ^ In file included from /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/bxzstr.hpp:20: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp: In function 'bxz::Compression bxz::detect_type(char*, char*)': /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp:33:19: warning: unused variable 'b3' [-Wunused-variable] 33 | unsigned char b3 = *reinterpret_cast< unsigned char * >(in_buff_start + 3); | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp:34:19: warning: unused variable 'b4' [-Wunused-variable] 34 | unsigned char b4 = *reinterpret_cast< unsigned char * >(in_buff_start + 4); | ^~ /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-sdk/../../tools/loaders/sharq/bxzstr/compression_types.hpp:35:19: warning: unused variable 'b5' [-Wunused-variable] 35 | unsigned char b5 = *reinterpret_cast< unsigned char * >(in_buff_start + 5); | ^~ [ 99%] Linking CXX executable ../../../test-bin/test-sharq-writer cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sharq-writer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sharq-writer.dir/test-sharq-writer.cpp.o" -o ../../../test-bin/test-sharq-writer /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [ 99%] Built target test-sharq-writer [100%] Linking CXX executable ../../../test-bin/test-sharq-parser cd /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test/loaders/sharq && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-sharq-parser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sra-sdk-3.0.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-sharq-parser.dir/test-sharq-parser.cpp.o" -o ../../../test-bin/test-sharq-parser -lstdc++fs /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libkapp.a ../../../ilib/libtk-version.a /usr/lib/x86_64-linux-gnu/libktst.a /usr/lib/x86_64-linux-gnu/libncbi-vdb.so -lpthread -ldl -lm /usr/lib/x86_64-linux-gnu/libbz2.so -lre2 -labsl_string_view make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' [100%] Built target test-sharq-parser make[2]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' jh_build -O--buildsystem=cmake debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' cd obj-x86_64-linux-gnu && \ ctest --force-new-ctest-process --verbose -j1 -LE online UpdateCTestConfiguration from :/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 9 Start 9: Test_NGS_Python_install 9: Test command: /usr/bin/python3 "/build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-python/setup.py" "-q" "install" "--user" 9: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/ngs/ngs-python 9: Environment variables: 9: PYTHONUSERBASE=/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/tmp/python 9: Test timeout computed to be: 1500 9: /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 9: !! 9: 9: ******************************************************************************** 9: Please avoid running ``setup.py`` directly. 9: Instead, use pypa/build, pypa/installer or other 9: standards-based tools. 9: 9: See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 9: ******************************************************************************** 9: 9: !! 9: self.initialize_options() 9: /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. 9: !! 9: 9: ******************************************************************************** 9: Please avoid running ``setup.py`` and ``easy_install``. 9: Instead, use pypa/build, pypa/installer or other 9: standards-based tools. 9: 9: See https://github.com/pypa/setuptools/issues/917 for details. 9: ******************************************************************************** 9: 9: !! 9: self.initialize_options() 9: zip_safe flag not set; analyzing archive contents... 1/114 Test #9: Test_NGS_Python_install ......................... Passed 1.05 sec test 15 Start 15: Ngs_MakeDB 15: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/ngs-makedb 15: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test/data 15: Test timeout computed to be: 1500 15: Running 1 test case... 15: SparseFragmentBlobs (0 s) 15: 15: *** No errors detected (0 s total) 2/114 Test #15: Ngs_MakeDB ...................................... Passed 0.27 sec test 16 Start 16: Test_Ngs 16: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-ngs 16: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/ngs-vdb/test 16: Test timeout computed to be: 1500 16: 16: *** No errors detected (0 s total) 3/114 Test #16: Test_Ngs ........................................ Passed 0.02 sec test 32 Start 32: GeneralWriterTest 32: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-general-writer 32: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/libs/general-writer/test 32: Test timeout computed to be: 1500 32: CreateGw Success 32: --------------------------------- 32: addTable Success 32: --------------------------------- 32: addColumn Success 32: --------------------------------- 32: dbAddDatabase Success 32: --------------------------------- 32: dbAddTable Success 32: --------------------------------- 32: write Success 32: --------------------------------- 32: setDBMetadataNode Success 32: --------------------------------- 32: setTblMetadataNode Success 32: --------------------------------- 32: setColMetadataNode Success 32: --------------------------------- 32: setProgMsg Success 32: --------------------------------- 32: Attempting add table after endStream 32: state violation adding table 32: addTable correctly failed 32: endStream Success 32: --------------------------------- 4/114 Test #32: GeneralWriterTest ............................... Passed 0.02 sec test 33 Start 33: Ref-Variation-1.0 33: Test command: /usr/bin/sh "./have-access.sh" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "ref-variation" 33: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/test 33: Test timeout computed to be: 1500 33: ./have-access.sh: line 6: vdb-config: command not found 33: no access to repository, skipping ref-variation test... 5/114 Test #33: Ref-Variation-1.0 ............................... Passed 0.02 sec test 34 Start 34: Var-Expand-1.0 34: Test command: /usr/bin/sh "./have-access.sh" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "var-expand" 34: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/external/ref-variation/test 34: Test timeout computed to be: 1500 34: ./have-access.sh: line 6: vdb-config: command not found 34: no access to repository, skipping var-expand test... 6/114 Test #34: Var-Expand-1.0 .................................. Passed 0.05 sec test 35 Start 35: SearchBlockWhiteBox 35: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-searchblock 35: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/external/sra-search/test 35: Test timeout computed to be: 1500 35: Running 8 test cases... 35: FgrepDumb (0 s) 35: SearchFgrepBoyerMoore (0 s) 35: SearchFgrepAho (0 s) 35: SearchAgrepDP (0 s) 35: SearchNucStrstr_NoExpr_NoCoords (0 s) 35: SearchNucStrstr_NoExpr_Coords_NotSupported (0 s) 35: SearchNucStrstr_Expr_Coords (0 s) 35: SearchSmithWaterman_Coords_NotSupported (0 s) 35: 35: *** No errors detected (0 s total) 7/114 Test #35: SearchBlockWhiteBox ............................. Passed 0.03 sec test 38 Start 38: GeneralLoaderWhiteBox 38: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-general-loader 38: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 38: Test timeout computed to be: 1500 38: Unpacked protocol: Running 62 test cases... 38: EmptyInput (0 s) 38: ShortInput (0 s) 38: BadSignature (0 s) 38: BadEndianness (0 s) 38: ReverseEndianness (0 s) 38: LaterVersion (0 s) 38: BadSchemaFileName (0 s) 38: BadSchemaFileName_Long (0 s) 38: BadSchemaName (0 s) 38: BadSchemaName_Long (0 s) 38: BadTableName (0 s) 38: BadTableName_Long (0 s) 38: DuplicateTableId (0 s) 38: BadColumnName (0 s) 38: BadTableId (0 s) 38: DuplicateColumnName (0 s) 38: DuplicateColumnId (0 s) 38: NoOpenStreamEvent (0 s) 38: NoCloseStreamEvent (0 s) 38: NoColumns (0 s) 38: SoftwareName (0 s) 38: SoftwareName_BadVersion (0 s) 38: DBAddDatabase (0 s) 38: DBAddSubDatabase (0 s) 38: DBAddTable (0 s) 38: DBAddTableToSubDb (0 s) 38: DBMetadataNode (0 s) 38: SubDBMetadataNode (0 s) 38: TblMetadataNode (0 s) 38: ColMetadataNode (0 s) 38: NoData (0 s) 38: Chunk_BadColumnId (0 s) 38: WriteNoCommit (0 s) 38: CommitBadTableId (0 s) 38: OneColumnOneCellOneChunk (0 s) 38: OneColumnOneCellOneChunk_Long (0 s) 38: OneColumnOneCellManyChunks (0 s) 38: IntegerCompression_MinimumCompression (0 s) 38: IntegerCompression_MaximumCompression (0 s) 38: IntegerCompression_MultipleValues (0 s) 38: OneColumnDefaultNoWrite (0 s) 38: OneColumnDefaultNoWrite_Long (0 s) 38: MoveAhead (0 s) 38: OneColumnDefaultOverwite (0 s) 38: OneColumnChangeDefault (0 s) 38: OneColumnDataAndDefaultsMixed (0 s) 38: TwoColumnsFullRow (0 s) 38: TwoColumnsIncompleteRow (0 s) 38: TwoColumnsPartialRowWithDefaults (0 s) 38: TwoColumnsPartialRowWithDefaultsAndOverride (0 s) 38: EmptyDefault_String (0 s) 38: EmptyDefault_Int (0 s) 38: MultipleTables_Multiple_Columns_MultipleRows (0 s) 38: AdditionalSchemaIncludePaths_Single (0 s) 38: AdditionalSchemaIncludePaths_Multiple (0 s) 38: AdditionalSchemaFiles_Single (0 s) 38: AdditionalSchemaFiles_Multiple (0 s) 38: ErrorMessage (0 s) 38: ErrorMessage_Long (0 s) 38: LogMessage (0 s) 38: ProgressMessage (0 s) 38: TargetOverride (0 s) 38: 38: *** No errors detected (1 s total) 38: Packed protocol: Running 62 test cases... 38: EmptyInput (0 s) 38: ShortInput (0 s) 38: BadSignature (0 s) 38: BadEndianness (0 s) 38: ReverseEndianness (0 s) 38: LaterVersion (0 s) 38: BadSchemaFileName (0 s) 38: BadSchemaFileName_Long (0 s) 38: BadSchemaName (0 s) 38: BadSchemaName_Long (0 s) 38: BadTableName (0 s) 38: BadTableName_Long (0 s) 38: DuplicateTableId (0 s) 38: BadColumnName (0 s) 38: BadTableId (0 s) 38: DuplicateColumnName (0 s) 38: DuplicateColumnId (0 s) 38: NoOpenStreamEvent (0 s) 38: NoCloseStreamEvent (0 s) 38: NoColumns (0 s) 38: SoftwareName (0 s) 38: SoftwareName_BadVersion (0 s) 38: DBAddDatabase (0 s) 38: DBAddSubDatabase (0 s) 38: DBAddTable (0 s) 38: DBAddTableToSubDb (0 s) 38: DBMetadataNode (0 s) 38: SubDBMetadataNode (0 s) 38: TblMetadataNode (0 s) 38: ColMetadataNode (0 s) 38: NoData (0 s) 38: Chunk_BadColumnId (0 s) 38: WriteNoCommit (0 s) 38: CommitBadTableId (0 s) 38: OneColumnOneCellOneChunk (0 s) 38: OneColumnOneCellOneChunk_Long (0 s) 38: OneColumnOneCellManyChunks (0 s) 38: IntegerCompression_MinimumCompression (0 s) 38: IntegerCompression_MaximumCompression (0 s) 38: IntegerCompression_MultipleValues (0 s) 38: OneColumnDefaultNoWrite (0 s) 38: OneColumnDefaultNoWrite_Long (0 s) 38: MoveAhead (0 s) 38: OneColumnDefaultOverwite (0 s) 38: OneColumnChangeDefault (0 s) 38: OneColumnDataAndDefaultsMixed (0 s) 38: TwoColumnsFullRow (0 s) 38: TwoColumnsIncompleteRow (0 s) 38: TwoColumnsPartialRowWithDefaults (0 s) 38: TwoColumnsPartialRowWithDefaultsAndOverride (0 s) 38: EmptyDefault_String (0 s) 38: EmptyDefault_Int (0 s) 38: MultipleTables_Multiple_Columns_MultipleRows (0 s) 38: AdditionalSchemaIncludePaths_Single (0 s) 38: AdditionalSchemaIncludePaths_Multiple (0 s) 38: AdditionalSchemaFiles_Single (0 s) 38: AdditionalSchemaFiles_Multiple (0 s) 38: ErrorMessage (0 s) 38: ErrorMessage_Long (0 s) 38: LogMessage (0 s) 38: ProgressMessage (0 s) 38: TargetOverride (0 s) 38: 38: *** No errors detected (1 s total) 8/114 Test #38: GeneralLoaderWhiteBox ........................... Passed 3.33 sec test 39 Start 39: GWDumper 39: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-gw-dumper 39: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/loaders/general-loader/test 39: Test timeout computed to be: 1500 9/114 Test #39: GWDumper ........................................ Passed 0.02 sec test 40 Start 40: makeinputs 40: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/makeinputs 40: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 40: Test timeout computed to be: 1500 10/114 Test #40: makeinputs ...................................... Passed 0.03 sec test 41 Start 41: GeneralLoader-1.0-Basic-Unpacked 41: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1" "0" "-I/usr/include/ncbi-vdb" 41: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 41: Test timeout computed to be: 1500 41: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1 0 -I/usr/include/ncbi-vdb 41: running test case 1 41: cat input/1.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/load.stderr 41: Load succeeded, dumping and matching stdout 41: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1/dump.stderr 11/114 Test #41: GeneralLoader-1.0-Basic-Unpacked ................ Passed 0.78 sec test 42 Start 42: GeneralLoader-1.1-Basic-Packed 42: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1packed" "0" "-I/usr/include/ncbi-vdb" 42: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 42: Test timeout computed to be: 1500 42: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1packed 0 -I/usr/include/ncbi-vdb 42: running test case 1packed 42: cat input/1packed.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/load.stderr 42: Load succeeded, dumping and matching stdout 42: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1packed/dump.stderr 12/114 Test #42: GeneralLoader-1.1-Basic-Packed .................. Passed 0.50 sec test 43 Start 43: GeneralLoader-1.2-TargetDbOverride 43: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1override" "0" "-I/usr/include/ncbi-vdb --target actual/1override/db" 43: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 43: Test timeout computed to be: 1500 43: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1override 0 -I/usr/include/ncbi-vdb --target actual/1override/db 43: running test case 1override 43: cat input/1override.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb --target actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 43: Load succeeded, dumping and matching stdout 43: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr 13/114 Test #43: GeneralLoader-1.2-TargetDbOverride .............. Passed 0.69 sec test 44 Start 44: GeneralLoader-1.3-TargetDbOverrideShorthand 44: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "1override" "0" "-I/usr/include/ncbi-vdb -T actual/1override/db" 44: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 44: Test timeout computed to be: 1500 44: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 1override 0 -I/usr/include/ncbi-vdb -T actual/1override/db 44: running test case 1override 44: cat input/1override.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -T actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/load.stderr 44: Load succeeded, dumping and matching stdout 44: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/1override/dump.stderr 14/114 Test #44: GeneralLoader-1.3-TargetDbOverrideShorthand ..... Passed 0.66 sec test 45 Start 45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked 45: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "2" "3" "-I/usr/include/ncbi-vdb -L=err" 45: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 45: Test timeout computed to be: 1500 45: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 2 3 -I/usr/include/ncbi-vdb -L=err 45: running test case 2 45: cat input/2.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2/load.stderr 45: Load failed as expected, matching stderr 15/114 Test #45: GeneralLoader-2.0-ErrorMessageEvent-Unpacked .... Passed 0.40 sec test 46 Start 46: GeneralLoader-2.1-ErrorMessageEvent-Packed 46: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "2packed" "3" "-I/usr/include/ncbi-vdb -L=err" 46: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 46: Test timeout computed to be: 1500 46: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 2packed 3 -I/usr/include/ncbi-vdb -L=err 46: running test case 2packed 46: cat input/2packed.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb -L=err 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/2packed/load.stderr 46: Load failed as expected, matching stderr 16/114 Test #46: GeneralLoader-2.1-ErrorMessageEvent-Packed ...... Passed 0.39 sec test 47 Start 47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked 47: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "3" "0" "-I/usr/include/ncbi-vdb" 47: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 47: Test timeout computed to be: 1500 47: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 3 0 -I/usr/include/ncbi-vdb 47: running test case 3 47: cat input/3.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 47: Load succeeded, dumping and matching stdout 47: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr 17/114 Test #47: GeneralLoader-3.0-EmptyDefaultValues-Unpacked ... Passed 1.07 sec test 48 Start 48: GeneralLoader-3.1-EmptyDefaultValues-Packed 48: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "3" "0" "-I/usr/include/ncbi-vdb" 48: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 48: Test timeout computed to be: 1500 48: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 3 0 -I/usr/include/ncbi-vdb 48: running test case 3 48: cat input/3.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/load.stderr 48: Load succeeded, dumping and matching stdout 48: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/3/dump.stderr 18/114 Test #48: GeneralLoader-3.1-EmptyDefaultValues-Packed ..... Passed 0.61 sec test 49 Start 49: GeneralLoader-4.0-MoveAheadEvent-Unpacked 49: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "4" "0" "-I/usr/include/ncbi-vdb" 49: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 49: Test timeout computed to be: 1500 49: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 4 0 -I/usr/include/ncbi-vdb 49: running test case 4 49: cat input/4.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/load.stderr 49: Load succeeded, dumping and matching stdout 49: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4/dump.stderr 19/114 Test #49: GeneralLoader-4.0-MoveAheadEvent-Unpacked ....... Passed 1.03 sec test 50 Start 50: GeneralLoader-4.1-MoveAheadEvent-Packed 50: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "4packed" "0" "-I/usr/include/ncbi-vdb" 50: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 50: Test timeout computed to be: 1500 50: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 4packed 0 -I/usr/include/ncbi-vdb 50: running test case 4packed 50: cat input/4packed.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/load.stderr 50: Load succeeded, dumping and matching stdout 50: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/4packed/dump.stderr 20/114 Test #50: GeneralLoader-4.1-MoveAheadEvent-Packed ......... Passed 1.88 sec test 51 Start 51: GeneralLoader-5.0-IntegerConversion 51: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "5packed" "0" "-I/usr/include/ncbi-vdb" 51: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 51: Test timeout computed to be: 1500 51: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 5packed 0 -I/usr/include/ncbi-vdb 51: running test case 5packed 51: cat input/5packed.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/load.stderr 51: Load succeeded, dumping and matching stdout 51: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/db 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/5packed/dump.stderr 21/114 Test #51: GeneralLoader-5.0-IntegerConversion ............. Passed 0.71 sec test 52 Start 52: GeneralLoader-6.0-SoftwareName-Unpacked 52: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "6" "0" "-L=info -I/usr/include/ncbi-vdb" "SOFTWARE/formatter" 52: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 52: Test timeout computed to be: 1500 52: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 6 0 -L=info -I/usr/include/ncbi-vdb SOFTWARE/formatter 52: running test case 6 52: cat input/6.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/load.stderr 52: Load succeeded, dumping and matching stdout 52: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/db SOFTWARE/formatter 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6/dump.stderr 22/114 Test #52: GeneralLoader-6.0-SoftwareName-Unpacked ......... Passed 0.49 sec test 53 Start 53: GeneralLoader-6.1-SoftwareName-Packed 53: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test" "6packed" "0" "-L=info -I/usr/include/ncbi-vdb" "SOFTWARE/formatter" 53: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 53: Test timeout computed to be: 1500 53: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/runtestcase.sh /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-config /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test 6packed 0 -L=info -I/usr/include/ncbi-vdb SOFTWARE/formatter 53: running test case 6packed 53: cat input/6packed.gl | /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader -L=info -I/usr/include/ncbi-vdb 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/load.stderr 53: Load succeeded, dumping and matching stdout 53: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/kdbmeta /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/db SOFTWARE/formatter 1>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stdout 2>/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/actual/6packed/dump.stderr 23/114 Test #53: GeneralLoader-6.1-SoftwareName-Packed ........... Passed 0.41 sec test 54 Start 54: bio-end-makeinputs 54: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/bio-end-makeinputs 54: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 54: Test timeout computed to be: 1500 24/114 Test #54: bio-end-makeinputs .............................. Passed 0.03 sec test 55 Start 55: BioEnd-Excl-1 55: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-1" "0" "n" "-I/usr/include/ncbi-vdb" "-L=debug" 55: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 55: Test timeout computed to be: 1500 55: running test bio-end:excl-1 25/114 Test #55: BioEnd-Excl-1 ................................... Passed 0.47 sec test 56 Start 56: BioEnd-Excl-2 56: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-2" "0" "n" "-I/usr/include/ncbi-vdb" 56: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 56: Test timeout computed to be: 1500 56: running test bio-end:excl-2 26/114 Test #56: BioEnd-Excl-2 ................................... Passed 0.32 sec test 57 Start 57: BioEnd-Excl-3 57: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-3" "0" "n" "-I/usr/include/ncbi-vdb" 57: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 57: Test timeout computed to be: 1500 57: running test bio-end:excl-3 27/114 Test #57: BioEnd-Excl-3 ................................... Passed 0.33 sec test 58 Start 58: BioEnd-Excl-4 58: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-4" "0" "n" "-I/usr/include/ncbi-vdb" 58: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 58: Test timeout computed to be: 1500 58: running test bio-end:excl-4 28/114 Test #58: BioEnd-Excl-4 ................................... Passed 0.46 sec test 59 Start 59: BioEnd-Incl-1 59: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "incl-1" "0" "n" "-I/usr/include/ncbi-vdb" 59: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 59: Test timeout computed to be: 1500 59: running test bio-end:incl-1 29/114 Test #59: BioEnd-Incl-1 ................................... Passed 0.47 sec test 60 Start 60: IdxText-CI-1 60: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "bio-end" "excl-1" "0" "n" "-I/usr/include/ncbi-vdb" 60: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 60: Test timeout computed to be: 1500 60: running test bio-end:excl-1 30/114 Test #60: IdxText-CI-1 .................................... Passed 0.38 sec test 61 Start 61: idx-text-makeinputs 61: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-makeinputs 61: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 61: Test timeout computed to be: 1500 31/114 Test #61: idx-text-makeinputs ............................. Passed 0.02 sec test 62 Start 62: IdxText-ci-1 62: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-1" "0" "y" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 62: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 62: Test timeout computed to be: 1500 62: running test idx-text:ci-1 32/114 Test #62: IdxText-ci-1 .................................... Passed 0.61 sec test 63 Start 63: IdxText-ci-2 63: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-2" "0" "y" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 63: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 63: Test timeout computed to be: 1500 63: running test idx-text:ci-2 33/114 Test #63: IdxText-ci-2 .................................... Passed 0.63 sec test 64 Start 64: IdxText-ci-3 64: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-3" "0" "y" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 64: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 64: Test timeout computed to be: 1500 64: running test idx-text:ci-3 34/114 Test #64: IdxText-ci-3 .................................... Passed 0.65 sec test 65 Start 65: IdxText-ci-4 65: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-4" "0" "y" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 65: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 65: Test timeout computed to be: 1500 65: running test idx-text:ci-4 35/114 Test #65: IdxText-ci-4 .................................... Passed 0.68 sec test 66 Start 66: IdxText-ci-5 66: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "ci-5" "0" "n" "-I/usr/include/ncbi-vdb" 66: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 66: Test timeout computed to be: 1500 66: running test idx-text:ci-5 36/114 Test #66: IdxText-ci-5 .................................... Passed 0.40 sec test 67 Start 67: IdxText-cs-1 67: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-1" "0" "y" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 67: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 67: Test timeout computed to be: 1500 67: running test idx-text:cs-1 37/114 Test #67: IdxText-cs-1 .................................... Passed 0.49 sec test 68 Start 68: IdxText-cs-2 68: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-2" "0" "y" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/idx-text-checklookup" "-I/usr/include/ncbi-vdb" 68: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 68: Test timeout computed to be: 1500 68: running test idx-text:cs-2 38/114 Test #68: IdxText-cs-2 .................................... Passed 0.51 sec test 69 Start 69: IdxText-cs-3 69: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/general-loader" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema" "idx-text" "cs-3" "0" "n" "-I/usr/include/ncbi-vdb" 69: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/loaders/general-loader/test/vschema 69: Test timeout computed to be: 1500 69: running test idx-text:cs-3 39/114 Test #69: IdxText-cs-3 .................................... Passed 0.39 sec test 70 Start 70: PileupStats-Version 70: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -V | grep --quiet `head -n 1 /build/reproducible-path/sra-sdk-3.0.3+dfsg/shared/toolkit.vers`" 70: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 70: Test timeout computed to be: 1500 40/114 Test #70: PileupStats-Version ............................. Passed 0.05 sec test 71 Start 71: PileupStats-Help 71: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -h | grep --quiet Usage" 71: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 71: Test timeout computed to be: 1500 41/114 Test #71: PileupStats-Help ................................ Passed 0.06 sec test 72 Start 72: PileupStats-NoArgs 72: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats; if [ $? == 0 ] ; then exit 1; fi;" 72: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 72: Test timeout computed to be: 1500 72: 72: Usage: 72: pileup-stats [options] 72: 72: Options: 72: -o|--output-file file for output 72: (default pipe to stdout) 72: -r|--remote-db name of remote database to create 72: (default .pileup_stat) 72: -x|--depth-cutoff cutoff for depth <= value (default 1) 72: -e|--event-cutoff cutoff for number of events > value (default 1) 72: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 72: -a|--align-category the types of alignments to pile up: 72: { primary, secondary, all } (default primary) 72: --buffer-size bytes size of output pipe buffer - default 32K bytes 72: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 72: -h|--help output brief explanation of the program 72: -v|--verbose increase the verbosity of the program. 72: -V|--version display the version of the program then quit. 72: use multiple times for more verbosity. 72: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 72: 72: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 72: 42/114 Test #72: PileupStats-NoArgs .............................. Passed 0.05 sec test 73 Start 73: PileupStats-IgnoreArgs-L 73: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -L 1; if [ $? == 0 ] ; then exit 1; fi;" 73: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 73: Test timeout computed to be: 1500 73: 73: Usage: 73: pileup-stats [options] 73: 73: Options: 73: -o|--output-file file for output 73: (default pipe to stdout) 73: -r|--remote-db name of remote database to create 73: (default .pileup_stat) 73: -x|--depth-cutoff cutoff for depth <= value (default 1) 73: -e|--event-cutoff cutoff for number of events > value (default 1) 73: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 73: -a|--align-category the types of alignments to pile up: 73: { primary, secondary, all } (default primary) 73: --buffer-size bytes size of output pipe buffer - default 32K bytes 73: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 73: -h|--help output brief explanation of the program 73: -v|--verbose increase the verbosity of the program. 73: -V|--version display the version of the program then quit. 73: use multiple times for more verbosity. 73: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 73: 73: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 73: 43/114 Test #73: PileupStats-IgnoreArgs-L ........................ Passed 0.01 sec test 74 Start 74: PileupStats-IgnoreArgs-z 74: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats -z ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 74: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 74: Test timeout computed to be: 1500 74: 74: Usage: 74: pileup-stats [options] 74: 74: Options: 74: -o|--output-file file for output 74: (default pipe to stdout) 74: -r|--remote-db name of remote database to create 74: (default .pileup_stat) 74: -x|--depth-cutoff cutoff for depth <= value (default 1) 74: -e|--event-cutoff cutoff for number of events > value (default 1) 74: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 74: -a|--align-category the types of alignments to pile up: 74: { primary, secondary, all } (default primary) 74: --buffer-size bytes size of output pipe buffer - default 32K bytes 74: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 74: -h|--help output brief explanation of the program 74: -v|--verbose increase the verbosity of the program. 74: -V|--version display the version of the program then quit. 74: use multiple times for more verbosity. 74: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 74: 74: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 74: 44/114 Test #74: PileupStats-IgnoreArgs-z ........................ Passed 0.03 sec test 75 Start 75: PileupStats-IgnoreArgs-loglevel 75: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --log-level 1; if [ $? == 0 ] ; then exit 1; fi;" 75: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 75: Test timeout computed to be: 1500 75: 75: Usage: 75: pileup-stats [options] 75: 75: Options: 75: -o|--output-file file for output 75: (default pipe to stdout) 75: -r|--remote-db name of remote database to create 75: (default .pileup_stat) 75: -x|--depth-cutoff cutoff for depth <= value (default 1) 75: -e|--event-cutoff cutoff for number of events > value (default 1) 75: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 75: -a|--align-category the types of alignments to pile up: 75: { primary, secondary, all } (default primary) 75: --buffer-size bytes size of output pipe buffer - default 32K bytes 75: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 75: -h|--help output brief explanation of the program 75: -v|--verbose increase the verbosity of the program. 75: -V|--version display the version of the program then quit. 75: use multiple times for more verbosity. 75: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 75: 75: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 75: 45/114 Test #75: PileupStats-IgnoreArgs-loglevel ................. Passed 0.01 sec test 76 Start 76: PileupStats-IgnoreArgs-xmllog 76: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --xml-log ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 76: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 76: Test timeout computed to be: 1500 76: 76: Usage: 76: pileup-stats [options] 76: 76: Options: 76: -o|--output-file file for output 76: (default pipe to stdout) 76: -r|--remote-db name of remote database to create 76: (default .pileup_stat) 76: -x|--depth-cutoff cutoff for depth <= value (default 1) 76: -e|--event-cutoff cutoff for number of events > value (default 1) 76: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 76: -a|--align-category the types of alignments to pile up: 76: { primary, secondary, all } (default primary) 76: --buffer-size bytes size of output pipe buffer - default 32K bytes 76: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 76: -h|--help output brief explanation of the program 76: -v|--verbose increase the verbosity of the program. 76: -V|--version display the version of the program then quit. 76: use multiple times for more verbosity. 76: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 76: 76: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 76: 46/114 Test #76: PileupStats-IgnoreArgs-xmllog ................... Passed 0.02 sec test 77 Start 77: PileupStats-IgnoreArgs-xmllogfd 77: Test command: /usr/bin/sh "-c" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats --xml-log-fd ignore.txt; if [ $? == 0 ] ; then exit 1; fi;" 77: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/tools/test-tools/pileup-stats/test 77: Test timeout computed to be: 1500 77: 77: Usage: 77: pileup-stats [options] 77: 77: Options: 77: -o|--output-file file for output 77: (default pipe to stdout) 77: -r|--remote-db name of remote database to create 77: (default .pileup_stat) 77: -x|--depth-cutoff cutoff for depth <= value (default 1) 77: -e|--event-cutoff cutoff for number of events > value (default 1) 77: -p|--num-significant-bits number of significant bits for depth and counts to store (default 4) 77: -a|--align-category the types of alignments to pile up: 77: { primary, secondary, all } (default primary) 77: --buffer-size bytes size of output pipe buffer - default 32K bytes 77: -U|--unpack-integer don't pack integers in output pipe - uses more bandwidth 77: -h|--help output brief explanation of the program 77: -v|--verbose increase the verbosity of the program. 77: -V|--version display the version of the program then quit. 77: use multiple times for more verbosity. 77: --log-stderr log via stderr rather than general-writer API (default - general-writer API) 77: 77: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/pileup-stats : 3.0.3 77: 47/114 Test #77: PileupStats-IgnoreArgs-xmllogfd ................. Passed 0.04 sec test 78 Start 78: Test_NgsJava_lib_load 78: Test command: /usr/bin/java "-cp" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/test-ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/lib/ngs-java.jar:/build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java/junit-4.11.jar" "-Dvdb.System.loadLibrary=1" "-Dvdb.log=FINEST" "org.junit.runner.JUnitCore" "gov.nih.nlm.ncbi.ngs.ngs_test_lib_load" 78: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/ngs/ngs-java 78: Test timeout computed to be: 1500 78: JUnit version 4.11 78: ......... 78: Time: 0.272 78: 78: OK (9 tests) 78: 48/114 Test #78: Test_NgsJava_lib_load ........................... Passed 1.33 sec test 82 Start 82: Test_Drivertool_BuildVersion 82: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_BuildVersion 82: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 82: Test timeout computed to be: 1500 82: Test_Version passed. 49/114 Test #82: Test_Drivertool_BuildVersion .................... Passed 0.02 sec test 83 Start 83: Test_Drivertool_FilePath 83: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_FilePath 83: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 83: Test timeout computed to be: 1500 83: Running 26 test cases... 83: DefaultConstruct (0 s) 83: Construct_Cstring (0 s) 83: Construct_String (0 s) 83: CopyConstruct_Empty (0 s) 83: CopyConstruct (0 s) 83: Assign_Empty (0 s) 83: Assign (0 s) 83: Copy (0 s) 83: Split (0 s) 83: BaseName (0 s) 83: Append (0 s) 83: RemoveSuffix_0 (0 s) 83: RemoveSuffix (0 s) 83: RemoveSuffix_Ext (0 s) 83: RemoveSuffix_Oversized (0 s) 83: CWD (0 s) 83: Exists (0 s) 83: CWD_Append (0 s) 83: Exists_Static (0 s) 83: Readable (0 s) 83: IsSame_Directory (0 s) 83: NotIsSame_Directory (0 s) 83: IsSame_File (0 s) 83: NotIsSame_File (0 s) 83: Current_Executable (0 s) 83: Executable_Yes (0 s) 83: 83: *** No errors detected (0 s total) 50/114 Test #83: Test_Drivertool_FilePath ........................ Passed 0.03 sec test 84 Start 84: Test_Drivertool_CommandLine 84: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_CommandLine 84: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 84: Test timeout computed to be: 1500 84: Test_CommandLine passed. 51/114 Test #84: Test_Drivertool_CommandLine ..................... Passed 0.02 sec test 85 Start 85: Test_Drivertool_JsonParsing 85: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_JsonParsing 85: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 85: Test timeout computed to be: 1500 52/114 Test #85: Test_Drivertool_JsonParsing ..................... Passed 0.06 sec test 86 Start 86: Test_Drivertool_SDLResponse 86: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_SDLResponse 86: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 86: Test timeout computed to be: 1500 53/114 Test #86: Test_Drivertool_SDLResponse ..................... Passed 0.02 sec test 87 Start 87: Test_Drivertool_Accession 87: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_Accession 87: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 87: Test timeout computed to be: 1500 54/114 Test #87: Test_Drivertool_Accession ....................... Passed 0.02 sec test 88 Start 88: Test_Drivertool_UUID 88: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Drivertool_UUID 88: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/driver-tool 88: Test timeout computed to be: 1500 55/114 Test #88: Test_Drivertool_UUID ............................ Passed 2.34 sec test 90 Start 90: Test_VDB_Config_model 90: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-config/model.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb-config-model" 90: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-config 90: Test timeout computed to be: 1500 90: testing /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-vdb-config-model 90: Running 11 test cases... 90: get_config_changed (0 s) 90: prefetch_download_to_cache (0 s) 90: user_accept_aws_charges (0 s) 90: user_accept_gcp_charges (0 s) 90: temp_cache_location (0 s) 90: gcp_credential_file_location (0 s) 90: aws_credential_file_location (0 s) 90: aws_profile (0 s) 90: noCommit (0 s) 90: Commit (0 s) 90: Reload (0 s) 90: 90: *** No errors detected (0 s total) 90: VDB Copy model test is finished 56/114 Test #90: Test_VDB_Config_model ........................... Passed 0.24 sec test 91 Start 91: Test_Vdb_dump_Check_exit_code 91: Test command: /usr/bin/cmake "-E" "env" "VDB_CONFIG=.." "/usr/bin/python3" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/build/check-exit-code.py" "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump" 91: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/external/vdb-dump 91: Test timeout computed to be: 1500 91: WARNING[TEST1] help message is in 'STDOUT' 91: [check-exit-code.py] test passed for [/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/vdb-dump] 57/114 Test #91: Test_Vdb_dump_Check_exit_code ................... Passed 0.39 sec test 93 Start 93: Test_KAPP_qfile 93: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_KAPP_qfile 93: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader 93: Test timeout computed to be: 1500 93: start-position : 0 93: queue-size : 1024 93: block-size : 0 93: chunk-size : 1024 58/114 Test #93: Test_KAPP_qfile ................................. Passed 0.02 sec test 94 Start 94: Test_LOADERFILE 94: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_LOADERFILE 94: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader 94: Test timeout computed to be: 1500 94: Running 5 test cases... 94: KQueueFile_ReadTimeout_FGsleeps (2 s) 94: KQueueFile_ReadTimeout_BGsleeps (3 s) 94: KQueueFile_WriteTimeout (2 s) 94: KLoaderFile_eolBeforeEof (0 s) 94: KLoaderFile_noEolBeforeEof (0 s) 94: 94: *** No errors detected (7 s total) 59/114 Test #94: Test_LOADERFILE ................................. Passed 7.09 sec test 95 Start 95: Test_LOADER 95: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_LOADER 95: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/loader 95: Test timeout computed to be: 1500 95: Running 2 test cases... 95: LoaderMeta_Write (0 s) 95: LoaderMeta_WriteWithVersion (0 s) 95: 95: *** No errors detected (0 s total) 60/114 Test #95: Test_LOADER ..................................... Passed 0.21 sec test 96 Start 96: Test_regexpr 96: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-regexpr 96: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 96: Test timeout computed to be: 1500 96: Running 4 test cases... 96: Construction (0 s) 96: LastInput (0 s) 96: NoMatch (0 s) 96: YesMatch (0 s) 96: 96: *** No errors detected (0 s total) 61/114 Test #96: Test_regexpr .................................... Passed 0.03 sec test 97 Start 97: Test_sharq_parser 97: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-sharq-parser 97: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 97: Test timeout computed to be: 1500 97: Running 93 test cases... 97: EmptyFile (0 s) 97: EndLines (0 s) 97: InvalidDefline (0 s) 97: InvalidDeflineError (0 s) 97: GoodRead (0 s) 97: GoodReadFollowedByJunk (0 s) 97: MultiLineRead (0 s) 97: NoLastLF (0 s) 97: InvalidSequence (0 s) 97: EmptyQuality (0 s) 97: EmptyQuality2 (0 s) 97: TestSequence (0 s) 97: TestSequence_Multi (0 s) 97: UridineTranslation (0 s) 97: IlluminaNew1 (0 s) 97: IlluminaNew2 (0 s) 97: IlluminaNew3 (0 s) 97: IlluminaNew4 (0 s) 97: IlluminaNew5 (0 s) 97: IlluminaNew6 (0 s) 97: IlluminaNew7 (0 s) 97: IlluminaNew8 (0 s) 97: IlluminaNew9 (0 s) 97: IlluminaNew10 (0 s) 97: IlluminaNew11 (0 s) 97: IlluminaNew12 (0 s) 97: IlluminaNew13 (0 s) 97: IlluminaNew14 (0 s) 97: IlluminaNew15 (0 s) 97: IlluminaNew16 (0 s) 97: IlluminaNew17 (0 s) 97: IlluminaNew18 (0 s) 97: IlluminaNew19 (0 s) 97: IlluminaNew20 (0 s) 97: IlluminaNew21 (0 s) 97: IlluminaNew22 (0 s) 97: IlluminaNewDataGroup1 (0 s) 97: BGI1 (0 s) 97: BGI2 (0 s) 97: BGI3 (0 s) 97: BGIOld1 (0 s) 97: BgiOld8 (0 s) 97: BgiNewd8 (0 s) 97: SequenceGetSpotGroupBarcode (0 s) 97: BarCode_Plus (0 s) 97: BarCode_Underscore (0 s) 97: NoColonAtTheEnd_Error (0 s) 97: SequenceGetSpotGroupUnderscore (0 s) 97: RetainIlluminaSuffix (0 s) 97: RetainBgiSuffix (0 s) 97: Test_get_next_spot_empty (0 s) 97: Test_get_next_spot (0 s) 97: Test_get_next_spot_multi_2 (0 s) 97: Test_get_next_spot_multi_1 (0 s) 97: Test_get_spot_empty (0 s) 97: Test_get_spot_no_match (0 s) 97: Test_get_spot_no_match2 (0 s) 97: Test_get_spot_match (0 s) 97: Test_get_spot_match_multi (0 s) 97: Test_get_spot_match_multi_skip (0 s) 97: Test_get_spot_match_multi_skip_2 (0 s) 97: IlluminaCasava_1_8 (0 s) 97: IlluminaCasava_1_8_SpotGroupNumber (0 s) 97: IlluminaCasava_1_8_SpotGroup_MoreMadness (0 s) 97: IlluminaCasava_1_8_EmptyTag (0 s) 97: Illumina_Underscore (0 s) 97: SRA192487 (0 s) 97: BgiNew8Digit (0 s) 97: Quality33TooLow (0 s) 97: Quality33Adjusteed (0 s) 97: Quality64TooLow (0 s) 97: Quality64Adjusted (0 s) 97: [2024-05-07 02:34:03.829] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length 97: TextQualityTruncated (0 s) 97: TextQualityAccepted (0 s) 97: TextQualityAdjusted (0 s) 97: [2024-05-07 02:34:03.836] [warning] [code:130] Read DG7PMJN1:293:D12THACXX:2:1101:1161:1968: quality score length exceeds sequence length 97: QualityTooLongTruncated (0 s) 97: Nanopore1_readno_early (0 s) 97: Nanopore1_readno_late (0 s) 97: Nanopore2 (0 s) 97: Nanopore3 (0 s) 97: Nanopore3_1 (0 s) 97: Nanopore4 (0 s) 97: Nanopore4_WithBarcode (0 s) 97: Nanopore4_WithBarcodeUnclassified (0 s) 97: Nanopore4_EmptyChannel (0 s) 97: Nanopore5 (0 s) 97: Nanopore_DefaultReadno (0 s) 97: Nanopore_ReadNoIsAFile (0 s) 97: Nanopore_ReadFilter_Default (0 s) 97: Nanopore_ReadFilter_Pass (0 s) 97: Nanopore_ReadFilter_Fail (0 s) 97: Nanopore_Barcode_BC (0 s) 97: Nanopore_Barcode_Edit (0 s) 97: 97: *** No errors detected (0 s total) 62/114 Test #97: Test_sharq_parser ............................... Passed 0.29 sec test 98 Start 98: Test_sharq_writer 98: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/test-sharq-writer 98: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 98: Test timeout computed to be: 1500 98: Running 7 test cases... 98: Construct (0 s) 98: SetAttr (0 s) 98: Destination (0 s) 98: DefaultSchema (0 s) 98: IlluminaSchema (0 s) 98: NanoporeSchema (0 s) 98: NanoporeSpecificColumns (0 s) 98: 98: *** No errors detected (0 s total) 63/114 Test #98: Test_sharq_writer ............................... Passed 0.01 sec test 99 Start 99: Test_001.read.supported 99: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.supported" "0" "0" "--debug" "--no-timestamp" "input/001.R1.fastq" 99: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 99: Test timeout computed to be: 1500 99: running 001.read.supported 99: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/001.R1.fastq 1>./actual/001.read.supported/load.stdout 2>./actual/001.read.supported/load.stderr 64/114 Test #99: Test_001.read.supported ......................... Passed 0.12 sec test 100 Start 100: Test_001.read.unsupported 100: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.unsupported" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.unsupported.fq" 100: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 100: Test timeout computed to be: 1500 100: running 001.read.unsupported 100: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.unsupported.fq 1>./actual/001.read.unsupported/load.stdout 2>./actual/001.read.unsupported/load.stderr 65/114 Test #100: Test_001.read.unsupported ....................... Passed 0.12 sec test 101 Start 101: Test_001.read.no_sequence 101: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.no_sequence" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.no_sequence.fq" 101: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 101: Test timeout computed to be: 1500 101: running 001.read.no_sequence 101: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_sequence.fq 1>./actual/001.read.no_sequence/load.stdout 2>./actual/001.read.no_sequence/load.stderr 66/114 Test #101: Test_001.read.no_sequence ....................... Passed 0.09 sec test 102 Start 102: Test_001.read.invalid_sequence 102: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_sequence" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.invalid_sequence.fq" 102: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 102: Test timeout computed to be: 1500 102: running 001.read.invalid_sequence 102: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.invalid_sequence.fq 1>./actual/001.read.invalid_sequence/load.stdout 2>./actual/001.read.invalid_sequence/load.stderr 67/114 Test #102: Test_001.read.invalid_sequence .................. Passed 0.08 sec test 103 Start 103: Test_001.read.no_quality 103: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.no_quality" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.no_quality.fq" 103: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 103: Test timeout computed to be: 1500 103: running 001.read.no_quality 103: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_quality.fq 1>./actual/001.read.no_quality/load.stdout 2>./actual/001.read.no_quality/load.stderr 68/114 Test #103: Test_001.read.no_quality ........................ Passed 0.11 sec test 104 Start 104: Test_001.read.no_quality_2 104: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.no_quality_2" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.no_quality_2.fq" 104: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 104: Test timeout computed to be: 1500 104: running 001.read.no_quality_2 104: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.no_quality_2.fq 1>./actual/001.read.no_quality_2/load.stdout 2>./actual/001.read.no_quality_2/load.stderr 69/114 Test #104: Test_001.read.no_quality_2 ...................... Passed 0.09 sec test 105 Start 105: Test_001.read.invalid_quality33 105: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_quality33" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 --quality=33 input/001.read.invalid_quality33.fq" 105: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 105: Test timeout computed to be: 1500 105: running 001.read.invalid_quality33 105: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=33 input/001.read.invalid_quality33.fq 1>./actual/001.read.invalid_quality33/load.stdout 2>./actual/001.read.invalid_quality33/load.stderr 70/114 Test #105: Test_001.read.invalid_quality33 ................. Passed 0.11 sec test 106 Start 106: Test_001.read.invalid_quality64 106: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_quality64" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 --quality=64 input/001.read.invalid_quality64.fq" 106: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 106: Test timeout computed to be: 1500 106: running 001.read.invalid_quality64 106: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=64 input/001.read.invalid_quality64.fq 1>./actual/001.read.invalid_quality64/load.stdout 2>./actual/001.read.invalid_quality64/load.stderr 71/114 Test #106: Test_001.read.invalid_quality64 ................. Passed 0.11 sec test 107 Start 107: Test_001.read.invalid_quality0 107: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.invalid_quality0" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 --quality=0 input/001.read.invalid_quality0.fq" 107: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 107: Test timeout computed to be: 1500 107: running 001.read.invalid_quality0 107: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --quality=0 input/001.read.invalid_quality0.fq 1>./actual/001.read.invalid_quality0/load.stdout 2>./actual/001.read.invalid_quality0/load.stderr 72/114 Test #107: Test_001.read.invalid_quality0 .................. Passed 0.11 sec test 108 Start 108: Test_001.read.long_quality 108: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.long_quality" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.long_quality.fq" 108: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 108: Test timeout computed to be: 1500 108: running 001.read.long_quality 108: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.long_quality.fq 1>./actual/001.read.long_quality/load.stdout 2>./actual/001.read.long_quality/load.stderr 73/114 Test #108: Test_001.read.long_quality ...................... Passed 0.11 sec test 109 Start 109: Test_001.read.bad_quality0 109: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.bad_quality0" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.bad_quality0.fq" 109: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 109: Test timeout computed to be: 1500 109: running 001.read.bad_quality0 109: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.bad_quality0.fq 1>./actual/001.read.bad_quality0/load.stdout 2>./actual/001.read.bad_quality0/load.stderr 74/114 Test #109: Test_001.read.bad_quality0 ...................... Passed 0.11 sec test 110 Start 110: Test_001.read.bad_quality33 110: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "001.read.bad_quality33" "1" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/001.read.bad_quality33.fq" 110: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 110: Test timeout computed to be: 1500 110: running 001.read.bad_quality33 110: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/001.read.bad_quality33.fq 1>./actual/001.read.bad_quality33/load.stdout 2>./actual/001.read.bad_quality33/load.stderr 75/114 Test #110: Test_001.read.bad_quality33 ..................... Passed 0.09 sec test 111 Start 111: Test_002.readTypes_default 111: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_default" "0" "0" "--debug" "--no-timestamp" "input/002.allBiological_1.fq input/002.allBiological_2.fq" 111: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 111: Test timeout computed to be: 1500 111: running 002.readTypes_default 111: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_default/load.stdout 2>./actual/002.readTypes_default/load.stderr 76/114 Test #111: Test_002.readTypes_default ...................... Passed 0.13 sec test 112 Start 112: Test_002.readTypes_technical 112: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_technical" "0" "0" "--debug" "--no-timestamp" "--readTypes=TT input/002.allBiological_1.fq input/002.allBiological_2.fq" 112: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 112: Test timeout computed to be: 1500 112: running 002.readTypes_technical 112: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TT input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_technical/load.stdout 2>./actual/002.readTypes_technical/load.stderr 77/114 Test #112: Test_002.readTypes_technical .................... Passed 0.16 sec test 113 Start 113: Test_002.readTypes_mixed 113: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_mixed" "0" "0" "--debug" "--no-timestamp" "--readTypes=TB input/002.allBiological_1.fq input/002.allBiological_2.fq" 113: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 113: Test timeout computed to be: 1500 113: running 002.readTypes_mixed 113: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TB input/002.allBiological_1.fq input/002.allBiological_2.fq 1>./actual/002.readTypes_mixed/load.stdout 2>./actual/002.readTypes_mixed/load.stderr 78/114 Test #113: Test_002.readTypes_mixed ........................ Passed 0.15 sec test 114 Start 114: Test_002.readTypes_missing 114: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_missing" "1" "0" "--debug" "--no-timestamp" "--read1PairFiles=input/001.R1.fastq" 114: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 114: Test timeout computed to be: 1500 114: running 002.readTypes_missing 114: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --read1PairFiles=input/001.R1.fastq 1>./actual/002.readTypes_missing/load.stdout 2>./actual/002.readTypes_missing/load.stderr 79/114 Test #114: Test_002.readTypes_missing ...................... Passed 0.09 sec test 115 Start 115: Test_002.readTypes_mismatch 115: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_mismatch" "1" "0" "--debug" "--no-timestamp" "--readTypes=TB --read1PairFiles=input/001.R1.fastq" 115: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 115: Test timeout computed to be: 1500 115: running 002.readTypes_mismatch 115: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=TB --read1PairFiles=input/001.R1.fastq 1>./actual/002.readTypes_mismatch/load.stdout 2>./actual/002.readTypes_mismatch/load.stderr 80/114 Test #115: Test_002.readTypes_mismatch ..................... Passed 0.12 sec test 116 Start 116: Test_002.readTypes_unexpected 116: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_unexpected" "1" "0" "--debug" "--no-timestamp" "--readTypes=X --read1PairFiles=input/002.allBiological_1.fq" 116: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 116: Test timeout computed to be: 1500 116: running 002.readTypes_unexpected 116: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=X --read1PairFiles=input/002.allBiological_1.fq 1>./actual/002.readTypes_unexpected/load.stdout 2>./actual/002.readTypes_unexpected/load.stderr 81/114 Test #116: Test_002.readTypes_unexpected ................... Passed 0.10 sec test 117 Start 117: Test_002.readTypes_interlaved_fail_1 117: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_interlaved_fail_1" "1" "0" "--debug" "--no-timestamp" "input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq" 117: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 117: Test timeout computed to be: 1500 117: running 002.readTypes_interlaved_fail_1 117: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_fail_1/load.stdout 2>./actual/002.readTypes_interlaved_fail_1/load.stderr 82/114 Test #117: Test_002.readTypes_interlaved_fail_1 ............ Passed 0.13 sec test 118 Start 118: Test_002.readTypes_interlaved_fail_2 118: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_interlaved_fail_2" "1" "0" "--debug" "--no-timestamp" "--readTypes=BB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq" 118: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 118: Test timeout computed to be: 1500 118: running 002.readTypes_interlaved_fail_2 118: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_fail_2/load.stdout 2>./actual/002.readTypes_interlaved_fail_2/load.stderr 83/114 Test #118: Test_002.readTypes_interlaved_fail_2 ............ Passed 0.15 sec test 119 Start 119: Test_002.readTypes_interlaved_pass 119: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "002.readTypes_interlaved_pass" "0" "0" "--debug" "--no-timestamp" "--readTypes=BTB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq" 119: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 119: Test timeout computed to be: 1500 119: running 002.readTypes_interlaved_pass 119: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BTB input/002.readTypes_interleaved_1.fq input/002.readTypes_interleaved_2.fq 1>./actual/002.readTypes_interlaved_pass/load.stdout 2>./actual/002.readTypes_interlaved_pass/load.stderr 84/114 Test #119: Test_002.readTypes_interlaved_pass .............. Passed 0.13 sec test 120 Start 120: Test_003.files_not_exists 120: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_not_exists" "1" "0" "--debug" "--no-timestamp" "dummy1.fq" 120: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 120: Test timeout computed to be: 1500 120: running 003.files_not_exists 120: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp dummy1.fq 1>./actual/003.files_not_exists/load.stdout 2>./actual/003.files_not_exists/load.stderr 85/114 Test #120: Test_003.files_not_exists ....................... Passed 0.09 sec test 121 Start 121: Test_003.files_not_valid 121: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_not_valid" "1" "0" "--debug" "--no-timestamp" "input/003.empty.fq" 121: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 121: Test timeout computed to be: 1500 121: running 003.files_not_valid 121: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.empty.fq 1>./actual/003.files_not_valid/load.stdout 2>./actual/003.files_not_valid/load.stderr 86/114 Test #121: Test_003.files_not_valid ........................ Passed 0.15 sec test 122 Start 122: Test_003.files_readpairs 122: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_readpairs" "0" "0" "--debug" "--no-timestamp" "--readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq" 122: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 122: Test timeout computed to be: 1500 122: running 003.files_readpairs 122: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq 1>./actual/003.files_readpairs/load.stdout 2>./actual/003.files_readpairs/load.stderr 87/114 Test #122: Test_003.files_readpairs ........................ Passed 0.22 sec test 123 Start 123: Test_003.files_mixed 123: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_mixed" "1" "0" "--debug" "--no-timestamp" "input/005.offset0_1.fq input/001.R1.fastq" 123: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 123: Test timeout computed to be: 1500 123: running 003.files_mixed 123: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset0_1.fq input/001.R1.fastq 1>./actual/003.files_mixed/load.stdout 2>./actual/003.files_mixed/load.stderr 88/114 Test #123: Test_003.files_mixed ............................ Passed 0.14 sec test 124 Start 124: Test_003.files_mixed_cluster 124: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_mixed_cluster" "1" "0" "--debug" "--no-timestamp" "input/003.t_R1.fastq input/003.t_I1.fastq input/001.R1.fastq" 124: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 124: Test timeout computed to be: 1500 124: running 003.files_mixed_cluster 124: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_R1.fastq input/003.t_I1.fastq input/001.R1.fastq 1>./actual/003.files_mixed_cluster/load.stdout 2>./actual/003.files_mixed_cluster/load.stderr 89/114 Test #124: Test_003.files_mixed_cluster .................... Passed 0.11 sec test 125 Start 125: Test_003.files_10x_mixed 125: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.files_10x_mixed" "1" "0" "--debug" "--no-timestamp" "input/003.t_I1.fastq input/003.t_R1.fastq input/003.t_R2.fastq input/003._I1.fastq input/003.R1.fastq input/003.R2.fastq" 125: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 125: Test timeout computed to be: 1500 125: running 003.files_10x_mixed 125: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_I1.fastq input/003.t_R1.fastq input/003.t_R2.fastq input/003._I1.fastq input/003.R1.fastq input/003.R2.fastq 1>./actual/003.files_10x_mixed/load.stdout 2>./actual/003.files_10x_mixed/load.stderr 90/114 Test #125: Test_003.files_10x_mixed ........................ Passed 0.14 sec test 126 Start 126: Test_003.readTypes_10x 126: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.readTypes_10x" "0" "0" "--debug" "--no-timestamp" "input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq" 126: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 126: Test timeout computed to be: 1500 126: running 003.readTypes_10x 126: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq 1>./actual/003.readTypes_10x/load.stdout 2>./actual/003.readTypes_10x/load.stderr 91/114 Test #126: Test_003.readTypes_10x .......................... Passed 0.16 sec test 127 Start 127: Test_003.wrong_pairing 127: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "003.wrong_pairing" "1" "0" "--debug" "--no-timestamp" "--readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq" 127: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 127: Test timeout computed to be: 1500 127: running 003.wrong_pairing 127: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq 1>./actual/003.wrong_pairing/load.stdout 2>./actual/003.wrong_pairing/load.stderr 92/114 Test #127: Test_003.wrong_pairing .......................... Passed 0.09 sec test 128 Start 128: Test_004.truncated.fail 128: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "004.truncated.fail" "1" "0" "--debug" "--no-timestamp" "input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz" 128: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 128: Test timeout computed to be: 1500 128: running 004.truncated.fail 128: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz 1>./actual/004.truncated.fail/load.stdout 2>./actual/004.truncated.fail/load.stderr 93/114 Test #128: Test_004.truncated.fail ......................... Passed 1.59 sec test 129 Start 129: Test_004.truncated.pass 129: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "004.truncated.pass" "0" "0" "--debug" "--no-timestamp" "--allowEarlyFileEnd input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz" 129: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 129: Test timeout computed to be: 1500 129: running 004.truncated.pass 129: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --allowEarlyFileEnd input/004.truncated_1.fq.gz input/004.truncated_2.fq.gz 1>./actual/004.truncated.pass/load.stdout 2>./actual/004.truncated.pass/load.stderr 94/114 Test #129: Test_004.truncated.pass ......................... Passed 2.02 sec test 130 Start 130: Test_005.offset0 130: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "005.offset0" "0" "0" "--debug" "--no-timestamp" "input/005.offset0_1.fq input/005.offset0_2.fq" 130: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 130: Test timeout computed to be: 1500 130: running 005.offset0 130: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset0_1.fq input/005.offset0_2.fq 1>./actual/005.offset0/load.stdout 2>./actual/005.offset0/load.stderr 95/114 Test #130: Test_005.offset0 ................................ Passed 0.12 sec test 131 Start 131: Test_005.offset64 131: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "005.offset64" "0" "0" "--debug" "--no-timestamp" "input/005.offset64_1.fq input/005.offset64_2.fq" 131: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 131: Test timeout computed to be: 1500 131: running 005.offset64 131: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/005.offset64_1.fq input/005.offset64_2.fq 1>./actual/005.offset64/load.stdout 2>./actual/005.offset64/load.stderr 96/114 Test #131: Test_005.offset64 ............................... Passed 0.11 sec test 132 Start 132: Test_006.duplicate 132: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "006.duplicate" "1" "0" "--debug" "--no-timestamp" "input/006.duplicate.fq" 132: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 132: Test timeout computed to be: 1500 132: running 006.duplicate 132: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/006.duplicate.fq 1>./actual/006.duplicate/load.stdout 2>./actual/006.duplicate/load.stderr 97/114 Test #132: Test_006.duplicate .............................. Passed 0.13 sec test 133 Start 133: Test_007.digest.udenfined 133: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.udenfined" "0" "0" "--debug" "--no-timestamp" "--digest input/001.read.unsupported.fq" 133: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 133: Test timeout computed to be: 1500 133: running 007.digest.udenfined 133: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/001.read.unsupported.fq 1>./actual/007.digest.udenfined/load.stdout 2>./actual/007.digest.udenfined/load.stderr 98/114 Test #133: Test_007.digest.udenfined ....................... Passed 0.10 sec test 134 Start 134: Test_007.digest.multiple 134: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.multiple" "0" "0" "--debug" "--no-timestamp" "--digest input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq" 134: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 134: Test timeout computed to be: 1500 134: running 007.digest.multiple 134: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/003.t_R1.fastq input/003.t_R1.fastq input/003.t_I1.fastq 1>./actual/007.digest.multiple/load.stdout 2>./actual/007.digest.multiple/load.stderr 99/114 Test #134: Test_007.digest.multiple ........................ Passed 0.12 sec test 135 Start 135: Test_007.digest.groups 135: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.groups" "0" "0" "--debug" "--no-timestamp" "--digest input/003.t_R1.fastq.gz input/003.t2_R1.fastq input/003.t3_R1.fastq input/003.t_R2.fastq.gz input/003.t2_R2.fastq input/003.t3_R2.fastq input/003.t_I1.fastq.gz input/003.t2_I1.fastq input/003.t3_I1.fastq" 135: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 135: Test timeout computed to be: 1500 135: running 007.digest.groups 135: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --digest input/003.t_R1.fastq.gz input/003.t2_R1.fastq input/003.t3_R1.fastq input/003.t_R2.fastq.gz input/003.t2_R2.fastq input/003.t3_R2.fastq input/003.t_I1.fastq.gz input/003.t2_I1.fastq input/003.t3_I1.fastq 1>./actual/007.digest.groups/load.stdout 2>./actual/007.digest.groups/load.stderr 100/114 Test #135: Test_007.digest.groups .......................... Passed 0.20 sec test 136 Start 136: Test_007.digest.error 136: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "007.digest.error" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 --digest input/001.read.invalid_quality0.fq" 136: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 136: Test timeout computed to be: 1500 136: running 007.digest.error 136: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 --digest input/001.read.invalid_quality0.fq 1>./actual/007.digest.error/load.stdout 2>./actual/007.digest.error/load.stderr 101/114 Test #136: Test_007.digest.error ........................... Passed 0.11 sec test 137 Start 137: Test_008.telemetry_pass 137: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "008.telemetry_pass" "0" "1" "--debug" "--no-timestamp" "--readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq" 137: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 137: Test timeout computed to be: 1500 137: running 008.telemetry_pass 137: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --readTypes=BBT --read1PairFiles=input/003.t_R1.fastq.gz,input/003.t2_R1.fastq,input/003.t3_R1.fastq --read2PairFiles=input/003.t_R2.fastq.gz,input/003.t2_R2.fastq,input/003.t3_R2.fastq --read3PairFiles=input/003.t_I1.fastq.gz,input/003.t2_I1.fastq,input/003.t3_I1.fastq -t ./actual/008.telemetry_pass/telemetry 1>./actual/008.telemetry_pass/load.stdout 2>./actual/008.telemetry_pass/load.stderr 102/114 Test #137: Test_008.telemetry_pass ......................... Passed 0.24 sec test 138 Start 138: Test_009.more_than_4_per_spot 138: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "009.more_than_4_per_spot" "1" "0" "--debug" "--no-timestamp" "--debug input/009.test_I1_001.fastq input/009.test_R1_001.fastq input/009.test_R2_001.fastq input/009.test_R3_001.fastq" 138: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 138: Test timeout computed to be: 1500 138: running 009.more_than_4_per_spot 138: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --debug input/009.test_I1_001.fastq input/009.test_R1_001.fastq input/009.test_R2_001.fastq input/009.test_R3_001.fastq 1>./actual/009.more_than_4_per_spot/load.stdout 2>./actual/009.more_than_4_per_spot/load.stderr 103/114 Test #138: Test_009.more_than_4_per_spot ................... Passed 0.18 sec test 139 Start 139: Test_010.errors.invalid_seq_pass1 139: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "010.errors.invalid_seq_pass1" "0" "0" "--debug" "--no-timestamp" "input/010.errors.invalid_seq.fq" 139: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 139: Test timeout computed to be: 1500 139: running 010.errors.invalid_seq_pass1 139: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_pass1/load.stdout 2>./actual/010.errors.invalid_seq_pass1/load.stderr 104/114 Test #139: Test_010.errors.invalid_seq_pass1 ............... Passed 0.10 sec test 140 Start 140: Test_010.errors.invalid_seq_pass2 140: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "010.errors.invalid_seq_pass2" "0" "0" "--debug" "--no-timestamp" "--max-err-count 5 input/010.errors.invalid_seq.fq" 140: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 140: Test timeout computed to be: 1500 140: running 010.errors.invalid_seq_pass2 140: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 5 input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_pass2/load.stdout 2>./actual/010.errors.invalid_seq_pass2/load.stderr 105/114 Test #140: Test_010.errors.invalid_seq_pass2 ............... Passed 0.09 sec test 141 Start 141: Test_010.errors.invalid_seq_fail 141: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "010.errors.invalid_seq_fail" "1" "0" "--debug" "--no-timestamp" "--max-err-count 3 input/010.errors.invalid_seq.fq" 141: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 141: Test timeout computed to be: 1500 141: running 010.errors.invalid_seq_fail 141: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 3 input/010.errors.invalid_seq.fq 1>./actual/010.errors.invalid_seq_fail/load.stdout 2>./actual/010.errors.invalid_seq_fail/load.stderr 106/114 Test #141: Test_010.errors.invalid_seq_fail ................ Passed 0.08 sec test 142 Start 142: Test_011.nanopore.3 142: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "011.nanopore.3" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/011.nanopore.3.fq" 142: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 142: Test timeout computed to be: 1500 142: running 011.nanopore.3 142: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/011.nanopore.3.fq 1>./actual/011.nanopore.3/load.stdout 2>./actual/011.nanopore.3/load.stderr 107/114 Test #142: Test_011.nanopore.3 ............................. Passed 0.12 sec test 143 Start 143: Test_012.qualities 143: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "012.qualities" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/012.test_I1_001.fastq input/012.test_R1_001.fastq input/012.test_R2_001.fastq input/012.test2_I1_001.fastq input/012.test2_R1_001.fastq input/012.test2_R2_001.fastq" 143: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 143: Test timeout computed to be: 1500 143: running 012.qualities 143: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/012.test_I1_001.fastq input/012.test_R1_001.fastq input/012.test_R2_001.fastq input/012.test2_I1_001.fastq input/012.test2_R1_001.fastq input/012.test2_R2_001.fastq 1>./actual/012.qualities/load.stdout 2>./actual/012.qualities/load.stderr 108/114 Test #143: Test_012.qualities .............................. Passed 0.20 sec test 144 Start 144: Test_013.no-reads 144: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq/runtestcase.sh "/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin" "sharq" "." "013.no-reads" "0" "0" "--debug" "--no-timestamp" "--max-err-count 0 input/013.t_I1.fastq input/013.t_I2.fastq input/013.t_R1.fastq input/013.t_R2.fastq" 144: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/loaders/sharq 144: Test timeout computed to be: 1500 144: running 013.no-reads 144: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/bin/sharq --debug --no-timestamp --max-err-count 0 input/013.t_I1.fastq input/013.t_I2.fastq input/013.t_R1.fastq input/013.t_R2.fastq 1>./actual/013.no-reads/load.stdout 2>./actual/013.no-reads/load.stderr 109/114 Test #144: Test_013.no-reads ............................... Passed 22.86 sec test 145 Start 145: Test_Align_samextract 145: Test command: /build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu/test-bin/Test_Align_samextract 145: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/internal/align 145: Test timeout computed to be: 1500 145: Running 14 test cases... 145: Test_Qual_Decode (0 s) 145: Fast_Sequence (0 s) 145: Fast_u32toa (0 s) 145: Fast_i32toa (0 s) 145: Fast_strtoi64 (0 s) 145: Decode_Cigar (0 s) 145: Check_Cigar (0 s) 145: In_Range (0 s) 145: Is_MD5 (0 s) 145: Is_floworder (0 s) 145: header1 (0 s) 145: BAMfile (0 s) 145: Filter (0 s) 145: None of below files should hang: 145: fuzz/id000000,sig11,src000036,ophavoc,rep128 145: fuzz/id000000,src000000+000001,opsplice,rep16 145: fuzz/id000000,src000000,oparith8,pos3,val+10 145: fuzz/id000001,src000001,oparith16,pos10,val-6 145: fuzz/id000001,src000001,oparith8,pos10,val+9 145: fuzz/id000001,src000003,ophavoc,rep2 145: fuzz/id000002,src000000+000006,opsplice,rep64 145: fuzz/id000002,src000001,oparith8,pos10,val-31 145: fuzz/id000002,src000001,ophavoc,rep4 145: fuzz/id000003,src000001,ophavoc,rep2 145: fuzz/id000003,src000001,ophavoc,rep8 145: fuzz/id000003,src000007,ophavoc,rep2 145: fuzz/id000004,src000001,ophavoc,rep2 145: fuzz/id000004,src000001,ophavoc,rep32 145: fuzz/id000004,src000012,ophavoc,rep8 145: fuzz/id000005,src000001,ophavoc,rep2 145: fuzz/id000005,src000001,ophavoc,rep8 145: fuzz/id000005,src000013+000012,opsplice,rep4 145: fuzz/id000006,src000001,ophavoc,rep2 145: fuzz/id000006,src000001,ophavoc,rep4 145: fuzz/id000006,src000014,ophavoc,rep2 145: fuzz/id000007,src000002,opflip1,pos4 145: fuzz/id000007,src000023,ophavoc,rep4 145: fuzz/id000008,src000002,opflip1,pos8 145: fuzz/id000008,src000029,ophavoc,rep64 145: fuzz/id000009,src000002,opflip1,pos22 145: fuzz/id000009,src000031,ophavoc,rep2 145: fuzz/id000010,src000002,opflip1,pos25 145: fuzz/id000010,src000037+000017,opsplice,rep2 145: fuzz/id000011,src000002,opflip1,pos33 145: fuzz/id000011,src000046,ophavoc,rep2 145: fuzz/id000012,src000002,opflip4,pos20 145: fuzz/id000012,src000049,ophavoc,rep4 145: fuzz/id000013,src000002,opflip4,pos38 145: fuzz/id000013,src000048,ophavoc,rep2 145: fuzz/id000014,src000002,opflip4,pos76 145: fuzz/id000014,src000021+000026,opsplice,rep2 145: fuzz/id000015,src000002,opflip8,pos25 145: fuzz/id000015,src000056,ophavoc,rep2 145: fuzz/id000016,src000002,opint16,pos77,val-129 145: fuzz/id000016,src000002,opint8,pos14,val-1 145: fuzz/id000017,src000002,ophavoc,rep32 145: fuzz/id000017,src000002,opint16,pos77,val-129 145: fuzz/id000018,src000002,opint32,pos25,val+2147483647 145: fuzz/id000018,src000003,opint16,pos3,val-129 145: fuzz/id000019,src000002,opint32,pos33,valbe-128 145: fuzz/id000019,src000007,opflip16,pos33 145: fuzz/id000020,src000002,ophavoc,rep4 145: fuzz/id000020,src000007,opint16,pos117,val-129 145: fuzz/id000021,src000004,opint16,pos4,val+32767 145: fuzz/id000021,src000011,opflip4,pos76 145: fuzz/id000022,src000004,ophavoc,rep16 145: fuzz/id000022,src000011,opflip4,pos116 145: fuzz/id000023,src000011,opflip4,pos116 145: fuzz/id000023,src000018,opflip1,pos15 145: fuzz/id000024,src000011,opflip16,pos52 145: fuzz/id000024,src000018,opflip1,pos26 145: fuzz/id000025,src000018,opflip1,pos15 145: fuzz/id000025,src000018,opflip4,pos92 145: fuzz/id000026,src000018,opflip1,pos26 145: fuzz/id000026,src000018,opflip4,pos137 145: fuzz/id000027,src000018,opflip4,pos24 145: fuzz/id000028,src000018,opflip4,pos92 145: fuzz/id000029,src000018,opflip4,pos137 145: fuzz/id000030,src000018,opint16,pos138,val-129 145: fuzz/id000031,src000018,ophavoc,rep8 145: 145: Fuzz_Hangs (0 s) 145: 145: *** No errors detected (1 s total) 110/114 Test #145: Test_Align_samextract ........................... Passed 1.20 sec test 147 Start 147: Test_Scripts_prepare-sra-names 147: Test command: /usr/bin/perl "test-prepare-sra-names.pl" 147: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/scripts 147: Test timeout computed to be: 1500 111/114 Test #147: Test_Scripts_prepare-sra-names .................. Passed 1.35 sec test 148 Start 148: Test_Scripts_fix-sra-names 148: Test command: /usr/bin/perl "test-fix-sra-names.pl" 148: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/scripts 148: Test timeout computed to be: 1500 112/114 Test #148: Test_Scripts_fix-sra-names ...................... Passed 0.59 sec test 149 Start 149: Test_Scripts_prepare-sra-names-py 149: Test command: /usr/bin/perl "test-prepare-sra-names-py.pl" 149: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/scripts 149: Test timeout computed to be: 1500 113/114 Test #149: Test_Scripts_prepare-sra-names-py ............... Passed 3.05 sec test 150 Start 150: Test_Scripts_fix-sra-names-py 150: Test command: /usr/bin/perl "test-fix-sra-names-py.pl" 150: Working Directory: /build/reproducible-path/sra-sdk-3.0.3+dfsg/test/scripts 150: Test timeout computed to be: 1500 114/114 Test #150: Test_Scripts_fix-sra-names-py ................... Passed 1.48 sec 100% tests passed, 0 tests failed out of 114 Total Test time (real) = 73.64 sec make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake debian/rules override_dh_prep make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_prep -X debian/tmp make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_auto_install cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/sra-sdk-3.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sra-sdk-3.0.3+dfsg -B/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" mkdir: cannot create directory '/usr/bin/ncbi': Permission denied cp: cannot create regular file '/usr/bin/ncbi/default.kfg': No such file or directory mkdir: cannot create directory '/usr/bin/ncbi': Permission denied cp: cannot create regular file '/usr/bin/ncbi/certs.kfg': No such file or directory mkdir: cannot create directory '/usr/bin/ncbi': Permission denied cp: cannot create regular file '/usr/bin/ncbi/vdb-copy.kfg': No such file or directory -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++.a -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-c++-static.a -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ncbi-vdb/NGS.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/FragTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/AlignTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/AlignSliceTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/PileupTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/RefTest.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/DumpReferenceFASTA.cpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/expected.txt -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/Makefile -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/share/examples/README.txt -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.a.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.a.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.a -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++-static.a -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.so.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libngs-c++.so -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.a.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.a.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.a -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs-static.a -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/PileupEventIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/ReferenceSequence.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/Reference.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/PileupEventIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReferenceSequence.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Reference.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Package.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Alignment.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Pileup.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/StringRef.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Fragment.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Read.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/PileupIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadGroup.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadGroupIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReferenceIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/FragmentIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/Statistics.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/PileupEvent.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/AlignmentIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/inl/ReadCollection.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/Package.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/Alignment.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/Pileup.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/StringRef.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/Fragment.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/Read.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/ErrorMsg.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/PileupIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/ReadGroup.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/ReadGroupIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/ReferenceIterator.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/Refcount.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceSequenceItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceSequenceItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/AlignmentItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReferenceItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/defs.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/FragmentItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StringItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/VTable.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadGroupItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadCollectionItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ErrBlock.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PackageItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ErrorMsg.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadGroupItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/Refcount.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StringItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/VTable.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ErrBlock.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/ReadCollectionItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PileupItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/AlignmentItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StatisticsItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/StatisticsItf.h -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/FragmentItf.hpp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/include/ngs/itf/PileupItf.h -- Installing: 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-dump -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-dump.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-dump-orig.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-dump.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-validate.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-validate.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-validate -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/check-corrupt.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/check-corrupt.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/check-corrupt -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-decrypt.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-decrypt.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-decrypt -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-encrypt.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-encrypt.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-encrypt -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/srapath -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/srapath.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/srapath-orig.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/srapath.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-stat.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-stat.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-stat -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ngs-pileup.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ngs-pileup.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ngs-pileup -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rcexplain.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rcexplain.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rcexplain -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdbmeta.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdbmeta.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdbmeta -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-info.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-info.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-info -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ref-variation.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ref-variation.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ref-variation -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/var-expand.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/var-expand.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/var-expand -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-search.3.0.3 -- Installing: 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/bam-load.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/bam-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/bam-load -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kar+.3 -- Installing: 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/build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-sort-cg.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-sort-cg.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sra-sort-cg -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/latf-load.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/latf-load.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/latf-load -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sharq.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sharq.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sharq -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sff-load.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sff-load.3 -- Installing: 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Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-cache.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/align-cache -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-sql.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-sql.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/vdb-sql -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/fastconv.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/fastconv.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/fastconv -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ccextract.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ccextract.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/ccextract -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/md5cp.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/md5cp.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/md5cp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-cmp.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-cmp.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-cmp -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-copy.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-copy.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/meta-copy -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/crc32sum.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/crc32sum.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/crc32sum -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-download.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-download.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/test-download -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdb-index.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdb-index.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/kdb-index -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-correct.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-correct.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pacbio-correct -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/schema-replace.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/schema-replace.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/schema-replace -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sortreadtest.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sortreadtest.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/sortreadtest -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rowwritetest.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rowwritetest.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/rowwritetest -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview-util.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview-util.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/samview-util -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/testld.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/testld.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/testld -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/txt2kdb.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/txt2kdb.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/txt2kdb -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pileup-stats.3.0.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pileup-stats.3 -- Installing: /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/bin/pileup-stats make[2]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg/obj-x86_64-linux-gnu' # build/install.sh /usr/include/ncbi-vdb/kfg/ncbi \ # /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy \ # debian/sra-toolkit/etc/ncbi \ # debian/sra-toolkit/etc/ncbi \ # debian/sra-toolkit/usr/bin \ # debian/sra-toolkit/usr/lib/x86_64-linux-gnu \ # /build/reproducible-path/sra-sdk-3.0.3+dfsg/shared/kfgsums build/install-kfg.sh default.kfg /usr/include/ncbi-vdb/kfg/ncbi debian/sra-toolkit/etc/ncbi \ /usr/include/ncbi-vdb/kfg/ncbi/kfgsums build/install-kfg.sh certs.kfg /usr/include/ncbi-vdb/kfg/ncbi debian/sra-toolkit/etc/ncbi \ /usr/include/ncbi-vdb/kfg/ncbi/kfgsums build/install-kfg.sh vdb-copy.kfg /build/reproducible-path/sra-sdk-3.0.3+dfsg/tools/internal/vdb-copy \ debian/sra-toolkit/etc/ncbi /build/reproducible-path/sra-sdk-3.0.3+dfsg/shared/kfgsums d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ --exclude-la \ --movedev "debian/*/usr/lib/x86_64-linux-gnu/libncbi-ngs.a*" \ usr/lib/x86_64-linux-gnu \ --override "s/libncbi-vdb3-dev/libncbi-vdb-dev/" \ debian/*/usr/lib/x86_64-linux-gnu/libncbi-ngs.so Library package automatic movement utility --> libncbi-vdb-dev package exists. set -e install -d -m 755 debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libncbi-ngs.so.3.0.3 debian/libncbi-ngs3/usr/lib/x86_64-linux-gnu PKGDEV=libncbi-ngs-dev PKGSHL=libncbi-ngs3 install -d -m 755 debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu mv debian/*/usr/lib/x86_64-linux-gnu/libncbi-ngs.a* debian/libncbi-ngs-dev/usr/lib/x86_64-linux-gnu d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ --exclude-la \ --movedev "debian/*/usr/lib/x86_64-linux-gnu/lib*c++.a*" \ usr/lib/x86_64-linux-gnu \ --movedev "debian/tmp/usr/include/*" usr/include \ --ignorelibdep \ debian/*/usr/lib/x86_64-linux-gnu/libngs-c++.so | \ tee /dev/stderr | LC_ALL=C grep '^[a-z]' | sh tee: /dev/stderr: Permission denied Error occurred, aborting make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' # upstream installs versioned *.a libs - we only want a single version for d in debian/lib*-dev/usr/lib/x86_64-linux-gnu ; do \ for slib in $d/lib*.a ; do \ mv $d/`readlink $slib` $slib ; \ mv $d/`readlink $slib` $slib ; \ done ; \ done ls -l debian/tmp/usr/bin total 81136 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 abi-dump -> abi-dump.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 abi-dump.3 -> abi-dump.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 269256 May 7 02:22 abi-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 abi-load -> abi-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 abi-load.3 -> abi-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 639104 May 7 02:23 abi-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 align-cache -> align-cache.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 17 May 7 02:34 align-cache.3 -> align-cache.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 249168 May 7 02:23 align-cache.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 align-info -> align-info.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 align-info.3 -> align-info.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 97352 May 7 02:23 align-info.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 bam-load -> bam-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 bam-load.3 -> bam-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 12582976 May 7 02:27 bam-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 cache-mgr -> cache-mgr.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 cache-mgr.3 -> cache-mgr.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 124752 May 7 02:23 cache-mgr.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 ccextract -> ccextract.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 ccextract.3 -> ccextract.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 273304 May 7 02:23 ccextract.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 cg-load -> cg-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 cg-load.3 -> cg-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 655560 May 7 02:23 cg-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 check-corrupt -> check-corrupt.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 19 May 7 02:34 check-corrupt.3 -> check-corrupt.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 239752 May 7 02:23 check-corrupt.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 copycat -> copycat.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 copycat.3 -> copycat.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 465248 May 7 02:23 copycat.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 crc32sum -> crc32sum.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 crc32sum.3 -> crc32sum.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 79240 May 7 02:23 crc32sum.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 22 May 7 02:34 dump-blob-boundaries -> dump-blob-boundaries.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 26 May 7 02:34 dump-blob-boundaries.3 -> dump-blob-boundaries.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 31528 May 7 02:23 dump-blob-boundaries.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 fastconv -> fastconv.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 fastconv.3 -> fastconv.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 4964168 May 7 02:27 fastconv.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 fasterq-dump -> fasterq-dump.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 826616 May 7 02:23 fasterq-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 fasterq-dump.3 -> fasterq-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 fasterq-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 fastq-dump -> fastq-dump.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 349448 May 7 02:23 fastq-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 fastq-dump.3 -> fastq-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 fastq-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 fastq-load -> fastq-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 fastq-load.3 -> fastq-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 694448 May 7 02:23 fastq-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 general-loader -> general-loader.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 20 May 7 02:34 general-loader.3 -> general-loader.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 1335776 May 7 02:24 general-loader.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 helicos-load -> helicos-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 helicos-load.3 -> helicos-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 605336 May 7 02:23 helicos-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 illumina-dump -> illumina-dump.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 19 May 7 02:34 illumina-dump.3 -> illumina-dump.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 251432 May 7 02:23 illumina-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 illumina-load -> illumina-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 19 May 7 02:34 illumina-load.3 -> illumina-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 654216 May 7 02:23 illumina-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 5 May 7 02:34 kar -> kar.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 6 May 7 02:34 kar+ -> kar+.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 kar+.3 -> kar+.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 237672 May 7 02:23 kar+.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 kar+meta -> kar+meta.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 kar+meta.3 -> kar+meta.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 158528 May 7 02:23 kar+meta.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 kar.3 -> kar.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 191472 May 7 02:23 kar.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 kdb-index -> kdb-index.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 kdb-index.3 -> kdb-index.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 78168 May 7 02:23 kdb-index.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 kdbmeta -> kdbmeta.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 kdbmeta.3 -> kdbmeta.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 124424 May 7 02:23 kdbmeta.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 latf-load -> latf-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 latf-load.3 -> latf-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 506696 May 7 02:24 latf-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 make-read-filter -> make-read-filter.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 22 May 7 02:34 make-read-filter.3 -> make-read-filter.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 153496 May 7 02:23 make-read-filter.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 7 May 7 02:34 md5cp -> md5cp.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 md5cp.3 -> md5cp.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 89600 May 7 02:23 md5cp.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 meta-cmp -> meta-cmp.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 meta-cmp.3 -> meta-cmp.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 81984 May 7 02:23 meta-cmp.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 meta-copy -> meta-copy.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 meta-copy.3 -> meta-copy.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 81952 May 7 02:23 meta-copy.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 ngs-pileup -> ngs-pileup.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 ngs-pileup.3 -> ngs-pileup.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 2548224 May 7 02:24 ngs-pileup.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 pacbio-correct -> pacbio-correct.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 20 May 7 02:34 pacbio-correct.3 -> pacbio-correct.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 75968 May 7 02:23 pacbio-correct.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 pacbio-load -> pacbio-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 17 May 7 02:34 pacbio-load.3 -> pacbio-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 477608 May 7 02:23 pacbio-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 pacbio-loadxml -> pacbio-loadxml.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 20 May 7 02:34 pacbio-loadxml.3 -> pacbio-loadxml.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 589024 May 7 02:23 pacbio-loadxml.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 pileup-stats -> pileup-stats.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 pileup-stats.3 -> pileup-stats.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 2728736 May 7 02:25 pileup-stats.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 prefetch -> prefetch.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 466528 May 7 02:24 prefetch-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 prefetch.3 -> prefetch.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 prefetch.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 rcexplain -> rcexplain.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 rcexplain.3 -> rcexplain.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 63344 May 7 02:23 rcexplain.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 20 May 7 02:34 read-filter-redact -> read-filter-redact.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 24 May 7 02:34 read-filter-redact.3 -> read-filter-redact.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 111536 May 7 02:23 read-filter-redact.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 ref-variation -> ref-variation.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 19 May 7 02:34 ref-variation.3 -> ref-variation.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 2909776 May 7 02:25 ref-variation.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 rowwritetest -> rowwritetest.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 rowwritetest.3 -> rowwritetest.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 88480 May 7 02:23 rowwritetest.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 sam-dump -> sam-dump.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 825832 May 7 02:23 sam-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sam-dump.3 -> sam-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sam-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 samview -> samview.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 samview-util -> samview-util.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 samview-util.3 -> samview-util.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 64120 May 7 02:23 samview-util.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 samview.3 -> samview.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 305368 May 7 02:23 samview.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 schema-replace -> schema-replace.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 20 May 7 02:34 schema-replace.3 -> schema-replace.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 82888 May 7 02:23 schema-replace.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 sff-dump -> sff-dump.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sff-dump.3 -> sff-dump.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 234472 May 7 02:23 sff-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 sff-load -> sff-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sff-load.3 -> sff-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 649728 May 7 02:23 sff-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 7 May 7 02:34 sharq -> sharq.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 11 May 7 02:34 sharq.3 -> sharq.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 17982008 May 7 02:29 sharq.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sortreadtest -> sortreadtest.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 sortreadtest.3 -> sortreadtest.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 79696 May 7 02:23 sortreadtest.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 sra-pileup -> sra-pileup.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 442536 May 7 02:23 sra-pileup-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 sra-pileup.3 -> sra-pileup.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sra-pileup.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 sra-search -> sra-search.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 sra-search.3 -> sra-search.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 3912072 May 7 02:25 sra-search.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 sra-sort -> sra-sort.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 sra-sort-cg -> sra-sort-cg.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 17 May 7 02:34 sra-sort-cg.3 -> sra-sort-cg.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 807376 May 7 02:23 sra-sort-cg.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sra-sort.3 -> sra-sort.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 807456 May 7 02:23 sra-sort.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 sra-stat -> sra-stat.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sra-stat.3 -> sra-stat.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 321856 May 7 02:23 sra-stat.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 srapath -> srapath.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 254848 May 7 02:23 srapath-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 srapath.3 -> srapath.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 srapath.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 sratools -> sratools.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 sratools.3 -> sratools.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 4906600 May 7 02:24 sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 srf-load -> srf-load.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 srf-load.3 -> srf-load.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 828992 May 7 02:23 srf-load.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 15 May 7 02:34 test-download -> test-download.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 19 May 7 02:34 test-download.3 -> test-download.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 93752 May 7 02:23 test-download.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 24 May 7 02:34 test-read-write-cursor -> test-read-write-cursor.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 28 May 7 02:34 test-read-write-cursor.3 -> test-read-write-cursor.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 75392 May 7 02:23 test-read-write-cursor.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 test-sra -> test-sra.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 test-sra.3 -> test-sra.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 334664 May 7 02:23 test-sra.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 8 May 7 02:34 testld -> testld.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 testld.3 -> testld.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 76400 May 7 02:23 testld.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 txt2kdb -> txt2kdb.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 txt2kdb.3 -> txt2kdb.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 82864 May 7 02:23 txt2kdb.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 var-expand -> var-expand.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 var-expand.3 -> var-expand.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 1987440 May 7 02:25 var-expand.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 vdb-config -> vdb-config.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 vdb-config.3 -> vdb-config.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 3475792 May 7 02:25 vdb-config.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 vdb-copy -> vdb-copy.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 vdb-copy.3 -> vdb-copy.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 328680 May 7 02:23 vdb-copy.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 vdb-decrypt -> vdb-decrypt.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 17 May 7 02:34 vdb-decrypt.3 -> vdb-decrypt.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 121648 May 7 02:23 vdb-decrypt.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 vdb-diff -> vdb-diff.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 vdb-diff.3 -> vdb-diff.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 155200 May 7 02:23 vdb-diff.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 vdb-dump -> vdb-dump.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 839216 May 7 02:23 vdb-dump-orig.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 vdb-dump.3 -> vdb-dump.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 vdb-dump.3.0.3 -> sratools.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 vdb-encrypt -> vdb-encrypt.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 17 May 7 02:34 vdb-encrypt.3 -> vdb-encrypt.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 119992 May 7 02:23 vdb-encrypt.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 10 May 7 02:34 vdb-lock -> vdb-lock.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 vdb-lock.3 -> vdb-lock.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 68296 May 7 02:23 vdb-lock.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 9 May 7 02:34 vdb-sql -> vdb-sql.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 13 May 7 02:34 vdb-sql.3 -> vdb-sql.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 5217328 May 7 02:27 vdb-sql.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 12 May 7 02:34 vdb-unlock -> vdb-unlock.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 16 May 7 02:34 vdb-unlock.3 -> vdb-unlock.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 68304 May 7 02:23 vdb-unlock.3.0.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 14 May 7 02:34 vdb-validate -> vdb-validate.3 lrwxrwxrwx 1 pbuilder2 pbuilder2 18 May 7 02:34 vdb-validate.3 -> vdb-validate.3.0.3 -rwxr-xr-x 1 pbuilder2 pbuilder2 227448 May 7 02:23 vdb-validate.3.0.3 cd debian/tmp/usr/bin && \ for bin in *-orig.* ; do \ base=${bin%-orig.*} && \ vbase=$(readlink "$(readlink $base)") && \ vdriver=$(readlink "$vbase") && \ mv -v $bin $base-orig && \ ln -snfv ${vdriver%%.[0-9]*} $vbase || exit $? ; \ done && \ for bin in *[a-z+] ; do \ bin2=$(readlink $bin) ; \ bin3=$(readlink "$bin2") ; \ case $bin2 in \ $bin.* ) rm -v $bin2 && mv -v $bin3 $bin || exit $? ;; \ esac ; \ done renamed 'fasterq-dump-orig.3.0.3' -> 'fasterq-dump-orig' 'fasterq-dump.3.0.3' -> 'sratools' renamed 'fastq-dump-orig.3.0.3' -> 'fastq-dump-orig' 'fastq-dump.3.0.3' -> 'sratools' renamed 'prefetch-orig.3.0.3' -> 'prefetch-orig' 'prefetch.3.0.3' -> 'sratools' renamed 'sam-dump-orig.3.0.3' -> 'sam-dump-orig' 'sam-dump.3.0.3' -> 'sratools' renamed 'sra-pileup-orig.3.0.3' -> 'sra-pileup-orig' 'sra-pileup.3.0.3' -> 'sratools' renamed 'srapath-orig.3.0.3' -> 'srapath-orig' 'srapath.3.0.3' -> 'sratools' renamed 'vdb-dump-orig.3.0.3' -> 'vdb-dump-orig' 'vdb-dump.3.0.3' -> 'sratools' removed 'abi-dump.3' renamed 'abi-dump.3.0.3' -> 'abi-dump' removed 'abi-load.3' renamed 'abi-load.3.0.3' -> 'abi-load' removed 'align-cache.3' renamed 'align-cache.3.0.3' -> 'align-cache' removed 'align-info.3' renamed 'align-info.3.0.3' -> 'align-info' removed 'bam-load.3' renamed 'bam-load.3.0.3' -> 'bam-load' removed 'cache-mgr.3' renamed 'cache-mgr.3.0.3' -> 'cache-mgr' removed 'ccextract.3' renamed 'ccextract.3.0.3' -> 'ccextract' removed 'cg-load.3' renamed 'cg-load.3.0.3' -> 'cg-load' removed 'check-corrupt.3' renamed 'check-corrupt.3.0.3' -> 'check-corrupt' removed 'copycat.3' renamed 'copycat.3.0.3' -> 'copycat' removed 'crc32sum.3' renamed 'crc32sum.3.0.3' -> 'crc32sum' removed 'dump-blob-boundaries.3' renamed 'dump-blob-boundaries.3.0.3' -> 'dump-blob-boundaries' removed 'fastconv.3' renamed 'fastconv.3.0.3' -> 'fastconv' removed 'fasterq-dump.3' renamed 'fasterq-dump.3.0.3' -> 'fasterq-dump' removed 'fastq-dump.3' renamed 'fastq-dump.3.0.3' -> 'fastq-dump' removed 'fastq-load.3' renamed 'fastq-load.3.0.3' -> 'fastq-load' removed 'general-loader.3' renamed 'general-loader.3.0.3' -> 'general-loader' removed 'helicos-load.3' renamed 'helicos-load.3.0.3' -> 'helicos-load' removed 'illumina-dump.3' renamed 'illumina-dump.3.0.3' -> 'illumina-dump' removed 'illumina-load.3' renamed 'illumina-load.3.0.3' -> 'illumina-load' removed 'kar.3' renamed 'kar.3.0.3' -> 'kar' removed 'kar+.3' renamed 'kar+.3.0.3' -> 'kar+' removed 'kar+meta.3' renamed 'kar+meta.3.0.3' -> 'kar+meta' removed 'kdb-index.3' renamed 'kdb-index.3.0.3' -> 'kdb-index' removed 'kdbmeta.3' renamed 'kdbmeta.3.0.3' -> 'kdbmeta' removed 'latf-load.3' renamed 'latf-load.3.0.3' -> 'latf-load' removed 'make-read-filter.3' renamed 'make-read-filter.3.0.3' -> 'make-read-filter' removed 'md5cp.3' renamed 'md5cp.3.0.3' -> 'md5cp' removed 'meta-cmp.3' renamed 'meta-cmp.3.0.3' -> 'meta-cmp' removed 'meta-copy.3' renamed 'meta-copy.3.0.3' -> 'meta-copy' removed 'ngs-pileup.3' renamed 'ngs-pileup.3.0.3' -> 'ngs-pileup' removed 'pacbio-correct.3' renamed 'pacbio-correct.3.0.3' -> 'pacbio-correct' removed 'pacbio-load.3' renamed 'pacbio-load.3.0.3' -> 'pacbio-load' removed 'pacbio-loadxml.3' renamed 'pacbio-loadxml.3.0.3' -> 'pacbio-loadxml' removed 'pileup-stats.3' renamed 'pileup-stats.3.0.3' -> 'pileup-stats' removed 'prefetch.3' renamed 'prefetch.3.0.3' -> 'prefetch' removed 'rcexplain.3' renamed 'rcexplain.3.0.3' -> 'rcexplain' removed 'read-filter-redact.3' renamed 'read-filter-redact.3.0.3' -> 'read-filter-redact' removed 'ref-variation.3' renamed 'ref-variation.3.0.3' -> 'ref-variation' removed 'rowwritetest.3' renamed 'rowwritetest.3.0.3' -> 'rowwritetest' removed 'sam-dump.3' renamed 'sam-dump.3.0.3' -> 'sam-dump' removed 'samview.3' renamed 'samview.3.0.3' -> 'samview' removed 'samview-util.3' renamed 'samview-util.3.0.3' -> 'samview-util' removed 'schema-replace.3' renamed 'schema-replace.3.0.3' -> 'schema-replace' removed 'sff-dump.3' renamed 'sff-dump.3.0.3' -> 'sff-dump' removed 'sff-load.3' renamed 'sff-load.3.0.3' -> 'sff-load' removed 'sharq.3' renamed 'sharq.3.0.3' -> 'sharq' removed 'sortreadtest.3' renamed 'sortreadtest.3.0.3' -> 'sortreadtest' removed 'sra-pileup.3' renamed 'sra-pileup.3.0.3' -> 'sra-pileup' removed 'sra-search.3' renamed 'sra-search.3.0.3' -> 'sra-search' removed 'sra-sort.3' renamed 'sra-sort.3.0.3' -> 'sra-sort' removed 'sra-sort-cg.3' renamed 'sra-sort-cg.3.0.3' -> 'sra-sort-cg' removed 'sra-stat.3' renamed 'sra-stat.3.0.3' -> 'sra-stat' removed 'srapath.3' renamed 'srapath.3.0.3' -> 'srapath' removed 'sratools.3' renamed 'sratools.3.0.3' -> 'sratools' removed 'srf-load.3' renamed 'srf-load.3.0.3' -> 'srf-load' removed 'test-download.3' renamed 'test-download.3.0.3' -> 'test-download' removed 'test-read-write-cursor.3' renamed 'test-read-write-cursor.3.0.3' -> 'test-read-write-cursor' removed 'test-sra.3' renamed 'test-sra.3.0.3' -> 'test-sra' removed 'testld.3' renamed 'testld.3.0.3' -> 'testld' removed 'txt2kdb.3' renamed 'txt2kdb.3.0.3' -> 'txt2kdb' removed 'var-expand.3' renamed 'var-expand.3.0.3' -> 'var-expand' removed 'vdb-config.3' renamed 'vdb-config.3.0.3' -> 'vdb-config' removed 'vdb-copy.3' renamed 'vdb-copy.3.0.3' -> 'vdb-copy' removed 'vdb-decrypt.3' renamed 'vdb-decrypt.3.0.3' -> 'vdb-decrypt' removed 'vdb-diff.3' renamed 'vdb-diff.3.0.3' -> 'vdb-diff' removed 'vdb-dump.3' renamed 'vdb-dump.3.0.3' -> 'vdb-dump' removed 'vdb-encrypt.3' renamed 'vdb-encrypt.3.0.3' -> 'vdb-encrypt' removed 'vdb-lock.3' renamed 'vdb-lock.3.0.3' -> 'vdb-lock' removed 'vdb-sql.3' renamed 'vdb-sql.3.0.3' -> 'vdb-sql' removed 'vdb-unlock.3' renamed 'vdb-unlock.3.0.3' -> 'vdb-unlock' removed 'vdb-validate.3' renamed 'vdb-validate.3.0.3' -> 'vdb-validate' mkdir debian/tmp/usr/lib/sra-toolkit mv debian/tmp/usr/bin/sratools debian/tmp/usr/lib/sra-toolkit for x in debian/tmp/usr/bin/*-orig; do \ mv -v $x debian/tmp/usr/lib/sra-toolkit ; \ ln -snfv ../lib/sra-toolkit/sratools ${x%-orig} ; \ done renamed 'debian/tmp/usr/bin/fasterq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fasterq-dump-orig' 'debian/tmp/usr/bin/fasterq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/fastq-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/fastq-dump-orig' 'debian/tmp/usr/bin/fastq-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/prefetch-orig' -> 'debian/tmp/usr/lib/sra-toolkit/prefetch-orig' 'debian/tmp/usr/bin/prefetch' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sam-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sam-dump-orig' 'debian/tmp/usr/bin/sam-dump' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/sra-pileup-orig' -> 'debian/tmp/usr/lib/sra-toolkit/sra-pileup-orig' 'debian/tmp/usr/bin/sra-pileup' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/srapath-orig' -> 'debian/tmp/usr/lib/sra-toolkit/srapath-orig' 'debian/tmp/usr/bin/srapath' -> '../lib/sra-toolkit/sratools' renamed 'debian/tmp/usr/bin/vdb-dump-orig' -> 'debian/tmp/usr/lib/sra-toolkit/vdb-dump-orig' 'debian/tmp/usr/bin/vdb-dump' -> '../lib/sra-toolkit/sratools' dh_install # remove susipcious file which is not executable and conflicts with package magic rm -f debian/*/usr/bin/magic # Formally supply a standard installation ID to satisfy sratools echo '/LIBS/GUID = "806b5c3b-0088-4732-8359-51630950d723"' >debian/sra-toolkit/etc/ncbi/debian.kfg set -e && for i in 3.12 3.11; do \ cd ngs/ngs-python; \ python$i ./setup.py install --install-layout=deb \ --root /build/reproducible-path/sra-sdk-3.0.3+dfsg/debian/python3-ngs; \ cd ../..; \ done /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/ngs/LibManager.py:123: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() find debian -name "*.pyc" -delete find debian -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' jh_installjavadoc -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_installexamples find debian/*/ -name .gitignore -delete make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_python3 -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake debian/rules execute_before_dh_link make[1]: Entering directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' # Putting the upstream version number (without the dfsg part) at the end of # symlink source in the -jni package. sed -e 's/\(#STRIPPED_UPSTREAM_VERSION#\)/\13.0.3+dfsg/' \ -e 's/#STRIPPED_UPSTREAM_VERSION#\(.*\)+dfsg[0-9]*/\1/' \ -e 's/\$[({]DEB_HOST_MULTIARCH[)}]/x86_64-linux-gnu/g' \ debian/libngs-jni.links.in > debian/libngs-jni.links make[1]: Leaving directory '/build/reproducible-path/sra-sdk-3.0.3+dfsg' dh_link -O--buildsystem=cmake jh_installlibs -O--buildsystem=cmake jh_classpath -O--buildsystem=cmake jh_manifest -O--buildsystem=cmake jh_exec -O--buildsystem=cmake jh_depends -O--buildsystem=cmake mh_installpoms -O--buildsystem=cmake mh_linkjars --skip-clean-poms -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: symbol KClientHttpResultRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol VFSManagerRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol VCursorOpenParentRead used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol VCursorGetBlobDirect used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol ctx_clear used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol KConfigMakeLocal used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol KRsrcGlobalInit used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol string_cmp used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol KMDataNodeRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: symbol VDatabaseRelease used by debian/libngs-c++3/usr/lib/x86_64-linux-gnu/libngs-c++.so.3.0.3 found in none of the libraries dpkg-shlibdeps: warning: 133 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Depends field of package libngs-jni: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libncbi-ngs-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'sra-toolkit' in '../sra-toolkit_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'sra-toolkit-dbgsym' in '../sra-toolkit-dbgsym_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libngs-c++3' in '../libngs-c++3_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libngs-c++3-dbgsym' in '../libngs-c++3-dbgsym_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libngs-c++-dev' in '../libngs-c++-dev_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libncbi-ngs3' in '../libncbi-ngs3_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libncbi-ngs3-dbgsym' in '../libncbi-ngs3-dbgsym_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libngs-java-doc' in '../libngs-java-doc_3.0.3+dfsg-7_all.deb'. dpkg-deb: building package 'libncbi-ngs-dev' in '../libncbi-ngs-dev_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libngs-jni' in '../libngs-jni_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'libngs-java' in '../libngs-java_3.0.3+dfsg-7_amd64.deb'. dpkg-deb: building package 'python3-ngs' in '../python3-ngs_3.0.3+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../sra-sdk_3.0.3+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../sra-sdk_3.0.3+dfsg-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1056693/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1056693 and its subdirectories I: Current time: Tue May 7 02:37:35 +14 2024 I: pbuilder-time-stamp: 1714999055